From edd0db0c69c2458f0ea56d8460f954b4fa1eeaa0 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Mon, 4 Mar 2024 19:42:16 +0100
Subject: [PATCH 01/25] Create HamamatsuCamera()

---
 .../hamamatsu_camera/hamamatsu_camera.py      | 192 ++++++++++++++++++
 1 file changed, 192 insertions(+)
 create mode 100644 catkit2/services/hamamatsu_camera/hamamatsu_camera.py

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
new file mode 100644
index 000000000..9fd95b695
--- /dev/null
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -0,0 +1,192 @@
+"""
+This module contains a service for Hamamatsu digital cameras.
+
+This service is a wrapper around the DCAM-SDK4.
+It provides a simple interface to control the camera and acquire images.
+"""
+import threading
+import numpy as np
+from catkit2.testbed.service import Service
+
+try:
+    sdk_path = os.environ.get('CATKIT_DCAM_SDK_PATH')
+    if sdk_path is not None:
+        sys.path.append(sdk_path)
+
+    import dcam
+except ImportError:
+    print('To use Hamamatsu cameras, you need to set the CATKIT_DCAM_SDK_PATH environment variable.')
+    raise
+
+
+class HamamatsuCamera(Service):
+    """
+    Service for Hamamatsu cameras.
+
+    This service is a wrapper around the DCAM-SDK4.
+    It provides a simple interface to control the camera and acquire images.
+
+    Attributes
+    ----------
+    cam : Camera
+        The camera to control.
+    pixel_formats : dict
+        A dictionary to store the pixel format and the corresponding numpy dtype and dcam pixel format.
+    current_pixel_format : str
+        The current pixel format to use.
+    temperature_thread : threading.Thread
+        A thread to monitor the temperature of the camera.
+    temperature : DataStream
+        A data stream to submit the temperature of the camera.
+    images : DataStream
+        A data stream to submit the images from the camera.
+    is_acquiring : DataStream
+        A data stream to submit whether the camera is currently acquiring images.
+    should_be_acquiring : threading.Event
+        An event to signal whether the camera should be acquiring images.
+    NUM_FRAMES : int
+        The number of frames to allocate for the data streams.
+
+    Methods
+    -------
+    open()
+        Open the service.
+    main()
+        The main function of the service.
+    close()
+        Close the service.
+    acquisition_loop()
+        The main acquisition loop.
+    monitor_temperature()
+        Monitor the temperature of the camera.
+    start_acquisition()
+        Start the acquisition loop.
+    end_acquisition()
+        End the acquisition loop.
+    get_temperature()
+        Get the temperature of the camera.
+    """
+    NUM_FRAMES = 20
+
+    def __init__(self):
+        """
+        Create a new HamamatsuCamera service.
+        """
+        super().__init__('hamamatsu_camera')
+
+        self.cam = None
+
+        # Dictionary to store the pixel format and the corresponding numpy dtype and dcam pixel format
+        self.pixel_formats = {
+            "Mono8": DCAM_PIXELTYPE.Mono8,
+            "Mono16": DCAM_PIXELTYPE.Mono16,
+        }
+        self.current_pixel_format = None
+        self.temperature_thread = None
+        self.temperature = None
+        self.images = None
+        self.is_acquiring = None
+
+        self.should_be_acquiring = threading.Event()
+        self.should_be_acquiring.set()
+
+    def open(self):
+        """
+        Open the service.
+
+        This function is called when the service is opened.
+        It initializes the camera and creates the data streams and properties.
+
+        Raises
+        ------
+        ValueError
+            If the pixel format is invalid.
+        """
+        dcam.Dcamapi.init()
+
+        camera_id = self.config.get('camera_id', 0)
+        self.cam = dcam.Dcam(camera_id)
+        self.log.info('Using camera with ID %s', camera_id)
+        self.cam.dev_open()
+
+        self.current_pixel_format = self.config.get('pixel_format', 'Mono16')
+        if self.current_pixel_format not in self.pixel_formats:
+            raise ValueError('Invalid pixel format: ' +
+                             self.current_pixel_format +
+                             ', must be one of ' +
+                             str(list(self.pixel_formats.keys())))
+        self.log.info('Using pixel format: %s', self.current_pixel_format)
+        # self.cam.set_pixel_format(self.pixel_formats[self.current_pixel_format])   # TODO
+
+        # Set device values from config file (set width and height before offsets)
+        offset_x = self.config.get('offset_x', 0)
+        offset_y = self.config.get('offset_y', 0)
+
+        self.width = self.config.get('width', self.sensor_width - offset_x)
+        self.height = self.config.get('height', self.sensor_height - offset_y)
+        self.offset_x = offset_x
+        self.offset_y = offset_y
+
+        self.gain = self.config.get('gain', 0)
+        self.exposure_time = self.config.get('exposure_time', 1000)
+        self.temperature = self.make_data_stream('temperature', 'float64', [1], 20)
+
+        # Create datastreams
+        # Use the full sensor size here to always allocate enough shared memory.
+        self.images = self.make_data_stream('images', 'float32', [self.sensor_height, self.sensor_width], self.NUM_FRAMES)
+
+        self.is_acquiring = self.make_data_stream('is_acquiring', 'int8', [1], self.NUM_FRAMES)
+        self.is_acquiring.submit_data(np.array([0], dtype='int8'))
+
+        # Create properties
+        def make_property_helper(name, read_only=False):
+            if read_only:
+                self.make_property(name, lambda: getattr(self, name))
+            else:
+                self.make_property(name, lambda: getattr(self, name), lambda val: setattr(self, name, val))
+
+        make_property_helper('exposure_time')
+        make_property_helper('gain')
+        make_property_helper('brightness')
+
+        make_property_helper('width')
+        make_property_helper('height')
+        make_property_helper('offset_x')
+        make_property_helper('offset_y')
+
+        make_property_helper('sensor_width', read_only=True)
+        make_property_helper('sensor_height', read_only=True)
+
+        make_property_helper('device_name', read_only=True)
+
+        self.make_command('start_acquisition', self.start_acquisition)
+        self.make_command('end_acquisition', self.end_acquisition)
+
+        self.temperature_thread = threading.Thread(target=self.monitor_temperature)
+        self.temperature_thread.start()
+
+    def main(self):
+        """
+        The main function of the service.
+
+        This function is called when the service is started.
+        It starts the acquisition loop and waits for incoming frames.
+        """
+        while not self.should_shut_down:
+            if self.should_be_acquiring.wait(0.05):
+                self.acquisition_loop()
+
+    def close(self):
+        """
+        Close the service.
+
+        This function is called when the service is closed.
+        It stops the acquisition loop and cleans up the camera and data streams.
+        """
+        self.cam.dev_close()
+        self.cam = None
+
+
+if __name__ == '__main__':
+    service = HamamatsuCamera()
+    service.run()

From 26160af62b348764399c27255b295bf626660498 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Mon, 4 Mar 2024 19:57:45 +0100
Subject: [PATCH 02/25] Add missing methods (WIP)

---
 .../hamamatsu_camera/hamamatsu_camera.py      | 296 ++++++++++++++++++
 1 file changed, 296 insertions(+)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 9fd95b695..6b7a876eb 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -186,6 +186,302 @@ def close(self):
         self.cam.dev_close()
         self.cam = None
 
+        dcam.Dcamapi.uninit()
+
+    def acquisition_loop(self):
+        """
+        The main acquisition loop.
+
+        This function is the main loop for acquiring images from the camera.
+        It starts the acquisition and then waits for incoming frames.
+        """
+        # Make sure the data stream has the right size and datatype.
+        has_correct_parameters = np.allclose(self.images.shape, [self.height, self.width])
+        if not has_correct_parameters:
+            self.images.update_parameters('float32', [self.height, self.width], self.NUM_FRAMES)
+
+        # Start acquisition.
+        self.cam.buf_alloc(self.NUM_FRAMES)
+        self.cam.cap_start()
+        self.is_acquiring.submit_data(np.array([1], dtype='int8'))
+
+        try:
+            while self.should_be_acquiring.is_set() and not self.should_shut_down:
+                img = self.cam.buf_getlastframedata()
+
+                # TODO: there might be some image manipulation needed here
+        finally:
+            # Stop acquisition.
+            self.cam.cap_stop()
+            self.cam.buf_release()
+            self.is_acquiring.submit_data(np.array([0], dtype='int8'))
+
+    def monitor_temperature(self):
+        """
+        Monitor the temperature of the camera.
+
+        This function is a separate thread that monitors the temperature of
+        the camera and submits the data to the temperature data stream.
+        """
+        while not self.should_shut_down:
+            temperature = self.get_temperature()
+            self.temperature.submit_data(np.array([temperature]))
+
+            self.sleep(0.1)
+
+    def start_acquisition(self):
+        """
+        Start the acquisition loop.
+
+        This function starts the acquisition loop.
+        """
+        self.should_be_acquiring.set()
+
+    def end_acquisition(self):
+        """
+        End the acquisition loop.
+
+        This function ends the acquisition loop.
+        """
+        self.should_be_acquiring.clear()
+
+    def get_temperature(self):
+        """
+        Get the temperature of the camera.
+
+        This function gets the temperature of the camera.
+
+        Returns
+        -------
+        float:
+            The temperature of the camera in degrees Celsius.
+        """
+        return self.cam.DeviceTemperature.get()   # TODO
+
+    @property
+    def exposure_time(self):
+        """
+        The exposure time in microseconds.
+
+        This property can be used to get the exposure time of the camera.
+
+        Returns:
+        --------
+        int:
+            The exposure time in microseconds.   # TODO
+        """
+        return self.cam.ExposureTime.get()   # TODO
+
+    @exposure_time.setter
+    def exposure_time(self, exposure_time: int):
+        """
+        Set the exposure time in microseconds.
+
+        This property can be used to set the exposure time of the camera.
+
+        Parameters
+        ----------
+        exposure_time : int
+            The exposure time in microseconds.   # TODO
+        """
+        self.cam.ExposureTime.set(exposure_time)   # TODO
+
+    @property
+    def gain(self):
+        """
+        The gain of the camera.
+
+        This property can be used to get the gain of the camera.
+
+        Returns:
+        --------
+        int:
+            The gain of the camera.
+        """
+        return self.cam.Gain.get()   # TODO
+
+    @gain.setter
+    def gain(self, gain: int):
+        """
+        Set the gain of the camera.
+
+        This property can be used to set the gain of the camera.
+
+        Parameters
+        ----------
+        gain : int
+            The gain of the camera.
+        """
+        self.cam.Gain.set(gain)   # TODO
+
+    @property
+    def brightness(self):
+        """
+        The brightness of the camera.
+
+        This property can be used to get the brightness of the camera.
+
+        Returns:
+        --------
+        int:
+            The brightness of the camera.
+        """
+        return self.cam.Brightness.get()   # TODO
+
+    @brightness.setter
+    def brightness(self, brightness: int):
+        """
+        Set the brightness of the camera.
+
+        This property can be used to set the brightness of the camera.
+
+        Parameters
+        ----------
+        brightness : int
+            The brightness of the camera.
+        """
+        self.cam.Brightness.set(brightness)   # TODO
+
+    @property
+    def sensor_width(self):
+        """
+        The width of the sensor in pixels.
+
+        This property can be used to get the width of the sensor in pixels.
+
+        Returns:
+        --------
+        int:
+            The width of the sensor in pixels.
+        """
+        return self.cam.SensorWidth.get()   # TODO
+
+    @property
+    def sensor_height(self):
+        """
+        The height of the sensor in pixels.
+
+        This property can be used to get the height of the sensor in pixels.
+
+        Returns:
+        --------
+        int:
+            The height of the sensor in pixels.
+        """
+        return self.cam.SensorHeight.get()   # TODO
+
+    @property
+    def width(self):
+        """
+        The width of the image in pixels.
+
+        This property can be used to get the width of the image in pixels.
+
+        Returns:
+        --------
+        int:
+            The width of the image in pixels.
+        """
+        return self.cam.Width.get()   # TODO
+
+    @width.setter
+    def width(self, width: int):
+        """
+        Set the width of the image in pixels.
+
+        This property can be used to set the width of the image in pixels.
+
+        Parameters
+        ----------
+        width : int
+            The width of the image in pixels.
+        """
+        self.cam.Width.set(width)   # TODO
+
+    @property
+    def height(self):
+        """
+        The height of the image in pixels.
+
+        This property can be used to get the height of the image in pixels.
+
+        Returns:
+        --------
+        int:
+            The height of the image in pixels.
+        """
+        return self.cam.Height.get()   # TODO
+
+    @height.setter
+    def height(self, height: int):
+        """
+        Set the height of the image in pixels.
+
+        This property can be used to set the height of the image in pixels.
+
+        Parameters
+        ----------
+        height : int
+            The height of the image in pixels.
+        """
+        self.cam.Height.set(height)   # TODO
+
+    @property
+    def offset_x(self):
+        """
+        The x offset of the image in pixels.
+
+        This property can be used to get the x offset of the image in pixels.
+
+        Returns:
+        --------
+        int:
+            The x offset of the image in pixels.
+        """
+        return self.cam.OffsetX.get()   # TODO
+
+    @offset_x.setter
+    def offset_x(self, offset_x: int):
+        """
+        Set the x offset of the image in pixels.
+
+        This property can be used to set the x offset of the image in pixels.
+
+        Parameters
+        ----------
+        offset_x : int
+            The x offset of the image in pixels.
+        """
+        self.cam.OffsetX.set(offset_x)   # TODO
+
+    @property
+    def offset_y(self):
+        """
+        The y offset of the image in pixels.
+
+        This property can be used to get the y offset of the image in pixels.
+
+        Returns:
+        --------
+        int:
+            The y offset of the image in pixels.
+        """
+        return self.cam.OffsetY.get()   # TODO
+
+    @offset_y.setter
+    def offset_y(self, offset_y: int):
+        """
+        Set the y offset of the image in pixels.
+
+        This property can be used to set the y offset of the image in pixels.
+
+        Parameters
+        ----------
+        offset_y : int
+            The y offset of the image in pixels.
+        """
+        self.cam.OffsetY.set(offset_y)   # TODO
+
 
 if __name__ == '__main__':
     service = HamamatsuCamera()

From 61bc82a2ad3b3f7da2f095f7a7ebd310b4f81536 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Mon, 4 Mar 2024 20:01:40 +0100
Subject: [PATCH 03/25] Add missing imports

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 6b7a876eb..fda9b95ba 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -4,6 +4,8 @@
 This service is a wrapper around the DCAM-SDK4.
 It provides a simple interface to control the camera and acquire images.
 """
+import os
+import sys
 import threading
 import numpy as np
 from catkit2.testbed.service import Service
@@ -78,8 +80,8 @@ def __init__(self):
 
         # Dictionary to store the pixel format and the corresponding numpy dtype and dcam pixel format
         self.pixel_formats = {
-            "Mono8": DCAM_PIXELTYPE.Mono8,
-            "Mono16": DCAM_PIXELTYPE.Mono16,
+            "Mono8": dcam.DCAM_PIXELTYPE.Mono8,
+            "Mono16": dcam.DCAM_PIXELTYPE.Mono16,
         }
         self.current_pixel_format = None
         self.temperature_thread = None

From 784337d45c58a00f94fb627e8cb574df4095fb45 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Mon, 4 Mar 2024 21:53:01 +0100
Subject: [PATCH 04/25] Get and set some of the properties

---
 .../hamamatsu_camera/hamamatsu_camera.py      | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index fda9b95ba..06f9c167f 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -118,7 +118,7 @@ def open(self):
                              ', must be one of ' +
                              str(list(self.pixel_formats.keys())))
         self.log.info('Using pixel format: %s', self.current_pixel_format)
-        # self.cam.set_pixel_format(self.pixel_formats[self.current_pixel_format])   # TODO
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.IMAGE_PIXELTYPE, self.pixel_formats[self.current_pixel_format])
 
         # Set device values from config file (set width and height before offsets)
         offset_x = self.config.get('offset_x', 0)
@@ -258,7 +258,7 @@ def get_temperature(self):
         float:
             The temperature of the camera in degrees Celsius.
         """
-        return self.cam.DeviceTemperature.get()   # TODO
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.SENSORTEMPERATURE)
 
     @property
     def exposure_time(self):
@@ -269,13 +269,13 @@ def exposure_time(self):
 
         Returns:
         --------
-        int:
-            The exposure time in microseconds.   # TODO
+        float:
+            The exposure time in seconds.
         """
-        return self.cam.ExposureTime.get()   # TODO
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.EXPOSURETIME)
 
     @exposure_time.setter
-    def exposure_time(self, exposure_time: int):
+    def exposure_time(self, exposure_time: float):
         """
         Set the exposure time in microseconds.
 
@@ -283,10 +283,10 @@ def exposure_time(self, exposure_time: int):
 
         Parameters
         ----------
-        exposure_time : int
-            The exposure time in microseconds.   # TODO
+        exposure_time : float
+            The exposure time in seconds.
         """
-        self.cam.ExposureTime.set(exposure_time)   # TODO
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.EXPOSURETIME, exposure_time)
 
     @property
     def gain(self):
@@ -356,7 +356,7 @@ def sensor_width(self):
         int:
             The width of the sensor in pixels.
         """
-        return self.cam.SensorWidth.get()   # TODO
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_WIDTH)   # TODO: Is this sensor or image width?
 
     @property
     def sensor_height(self):
@@ -370,7 +370,7 @@ def sensor_height(self):
         int:
             The height of the sensor in pixels.
         """
-        return self.cam.SensorHeight.get()   # TODO
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_HEIGHT)   # TODO: Is this sensor or image height?
 
     @property
     def width(self):

From 89f52d3a56cc07ec8d9b9b10b912c459b417e0bb Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Wed, 17 Apr 2024 16:47:31 +0200
Subject: [PATCH 05/25] Update service after initial lab tests

---
 .../hamamatsu_camera/hamamatsu_camera.py      | 52 +++++++++++++------
 1 file changed, 36 insertions(+), 16 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 06f9c167f..b087fdc22 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -104,12 +104,23 @@ def open(self):
         ValueError
             If the pixel format is invalid.
         """
-        dcam.Dcamapi.init()
+        if dcam.Dcamapi.init() is False:
+            raise RuntimeError(f'Dcamapi.init() fails with error {dcam.Dcamapi.lasterr()}')
 
         camera_id = self.config.get('camera_id', 0)
         self.cam = dcam.Dcam(camera_id)
         self.log.info('Using camera with ID %s', camera_id)
-        self.cam.dev_open()
+        if self.cam.dev_open() is False:
+            raise RuntimeError(f'Dcam.dev_open() fails with error {self.cam.lasterr()}')
+
+        # Set subarray mode
+        self.cam.prop_setvalue(4202832, 2.0)  # TODO: ? - 2.0 for subarray mode on
+
+        # Set binning
+        self.cam.prop_setvalue(4198672, 1.0)   # TODO: find DCAM keyword for this
+
+        # Set camera mode
+        dcam.prop_setvalue(4194576, 2.0)   # TODO: find DCAM keyword for this - 2.0 for "standard", 1.0 for "ultraquiet"
 
         self.current_pixel_format = self.config.get('pixel_format', 'Mono16')
         if self.current_pixel_format not in self.pixel_formats:
@@ -130,7 +141,7 @@ def open(self):
         self.offset_y = offset_y
 
         self.gain = self.config.get('gain', 0)
-        self.exposure_time = self.config.get('exposure_time', 1000)
+        self.exposure_time = self.config.get('exposure_time', 1)
         self.temperature = self.make_data_stream('temperature', 'float64', [1], 20)
 
         # Create datastreams
@@ -203,15 +214,22 @@ def acquisition_loop(self):
             self.images.update_parameters('float32', [self.height, self.width], self.NUM_FRAMES)
 
         # Start acquisition.
-        self.cam.buf_alloc(self.NUM_FRAMES)
-        self.cam.cap_start()
+        if self.cam.buf_alloc(self.NUM_FRAMES) is False:
+            raise RuntimeError(f'Dcam.buf_alloc() fails with error {self.cam.lasterr()}')
+        if self.cam.cap_start() is False:
+            raise RuntimeError(f'Dcam.cap_start() fails with error {self.cam.lasterr()}')
         self.is_acquiring.submit_data(np.array([1], dtype='int8'))
 
+        timeout_millisec = 2000
         try:
             while self.should_be_acquiring.is_set() and not self.should_shut_down:
+                if self.cam.lasterr().is_timeout():
+                    sself.log.warning('Timeout while waiting for frame')
+                if self.cam.wait_capevent_frameready(timeout_millisec) is False:
+                    raise RuntimeError(f'Dcam.wait_capevent_frameready() fails with error {self.cam.lasterr()}')
                 img = self.cam.buf_getlastframedata()
+                self.images.submit_data(img)
 
-                # TODO: there might be some image manipulation needed here
         finally:
             # Stop acquisition.
             self.cam.cap_stop()
@@ -263,7 +281,7 @@ def get_temperature(self):
     @property
     def exposure_time(self):
         """
-        The exposure time in microseconds.
+        The exposure time in seconds.
 
         This property can be used to get the exposure time of the camera.
 
@@ -277,7 +295,7 @@ def exposure_time(self):
     @exposure_time.setter
     def exposure_time(self, exposure_time: float):
         """
-        Set the exposure time in microseconds.
+        Set the exposure time in seconds.
 
         This property can be used to set the exposure time of the camera.
 
@@ -357,6 +375,7 @@ def sensor_width(self):
             The width of the sensor in pixels.
         """
         return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_WIDTH)   # TODO: Is this sensor or image width?
+        # TODO: needs to be 4325904 (sensor width) or 4325920 (sensor height)
 
     @property
     def sensor_height(self):
@@ -371,6 +390,7 @@ def sensor_height(self):
             The height of the sensor in pixels.
         """
         return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_HEIGHT)   # TODO: Is this sensor or image height?
+        # TODO: needs to be 4325904 (sensor width) or 4325920 (sensor height)
 
     @property
     def width(self):
@@ -384,7 +404,7 @@ def width(self):
         int:
             The width of the image in pixels.
         """
-        return self.cam.Width.get()   # TODO
+        return self.cam.prop_getvalue(4202784)  # TODO: find DCAM keyword for this
 
     @width.setter
     def width(self, width: int):
@@ -398,7 +418,7 @@ def width(self, width: int):
         width : int
             The width of the image in pixels.
         """
-        self.cam.Width.set(width)   # TODO
+        self.cam.prop_setvalue(4202784, width)  # TODO: find DCAM keyword for this
 
     @property
     def height(self):
@@ -412,7 +432,7 @@ def height(self):
         int:
             The height of the image in pixels.
         """
-        return self.cam.Height.get()   # TODO
+        return self.cam.prop_getvalue(4202816)  # TODO: find DCAM keyword for this
 
     @height.setter
     def height(self, height: int):
@@ -426,7 +446,7 @@ def height(self, height: int):
         height : int
             The height of the image in pixels.
         """
-        self.cam.Height.set(height)   # TODO
+        self.cam.prop_setvalue(4202816, height)  # TODO: find DCAM keyword for this
 
     @property
     def offset_x(self):
@@ -440,7 +460,7 @@ def offset_x(self):
         int:
             The x offset of the image in pixels.
         """
-        return self.cam.OffsetX.get()   # TODO
+        return self.cam.prop_getvalue(4202800)  # TODO: find DCAM keyword for this
 
     @offset_x.setter
     def offset_x(self, offset_x: int):
@@ -454,7 +474,7 @@ def offset_x(self, offset_x: int):
         offset_x : int
             The x offset of the image in pixels.
         """
-        self.cam.OffsetX.set(offset_x)   # TODO
+        self.cam.prop_setvalue(4202800, offset_x)  # TODO: find DCAM keyword for this
 
     @property
     def offset_y(self):
@@ -468,7 +488,7 @@ def offset_y(self):
         int:
             The y offset of the image in pixels.
         """
-        return self.cam.OffsetY.get()   # TODO
+        return self.cam.prop_getvalue(4202768)  # TODO: find DCAM keyword for this
 
     @offset_y.setter
     def offset_y(self, offset_y: int):
@@ -482,7 +502,7 @@ def offset_y(self, offset_y: int):
         offset_y : int
             The y offset of the image in pixels.
         """
-        self.cam.OffsetY.set(offset_y)   # TODO
+        self.cam.prop_setvalue(4202768, offset_x)  # TODO: find DCAM keyword for this
 
 
 if __name__ == '__main__':

From e0df7f22cd4da6c3ea153233c0df181f3b53bb73 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Wed, 17 Apr 2024 22:24:38 +0200
Subject: [PATCH 06/25] Replace property id numbers with named properties from
 DCAM_IDPROP

---
 .../hamamatsu_camera/hamamatsu_camera.py      | 30 +++++++++----------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index b087fdc22..992e9f57e 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -114,13 +114,13 @@ def open(self):
             raise RuntimeError(f'Dcam.dev_open() fails with error {self.cam.lasterr()}')
 
         # Set subarray mode
-        self.cam.prop_setvalue(4202832, 2.0)  # TODO: ? - 2.0 for subarray mode on
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYMODE, 2.0)  # TODO: ? - 2.0 for subarray mode on
 
         # Set binning
-        self.cam.prop_setvalue(4198672, 1.0)   # TODO: find DCAM keyword for this
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.BINNING, 1.0)  # TODO: read from config
 
         # Set camera mode
-        dcam.prop_setvalue(4194576, 2.0)   # TODO: find DCAM keyword for this - 2.0 for "standard", 1.0 for "ultraquiet"
+        dcam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, 2.0)   # TODO: read from config - 2.0 for "standard", 1.0 for "ultraquiet"
 
         self.current_pixel_format = self.config.get('pixel_format', 'Mono16')
         if self.current_pixel_format not in self.pixel_formats:
@@ -224,7 +224,7 @@ def acquisition_loop(self):
         try:
             while self.should_be_acquiring.is_set() and not self.should_shut_down:
                 if self.cam.lasterr().is_timeout():
-                    sself.log.warning('Timeout while waiting for frame')
+                    self.log.warning('Timeout while waiting for frame')
                 if self.cam.wait_capevent_frameready(timeout_millisec) is False:
                     raise RuntimeError(f'Dcam.wait_capevent_frameready() fails with error {self.cam.lasterr()}')
                 img = self.cam.buf_getlastframedata()
@@ -374,8 +374,7 @@ def sensor_width(self):
         int:
             The width of the sensor in pixels.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_WIDTH)   # TODO: Is this sensor or image width?
-        # TODO: needs to be 4325904 (sensor width) or 4325920 (sensor height)
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_WIDTH)
 
     @property
     def sensor_height(self):
@@ -389,8 +388,7 @@ def sensor_height(self):
         int:
             The height of the sensor in pixels.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_HEIGHT)   # TODO: Is this sensor or image height?
-        # TODO: needs to be 4325904 (sensor width) or 4325920 (sensor height)
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_HEIGHT)
 
     @property
     def width(self):
@@ -404,7 +402,7 @@ def width(self):
         int:
             The width of the image in pixels.
         """
-        return self.cam.prop_getvalue(4202784)  # TODO: find DCAM keyword for this
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.SUBARRAYHSIZE)
 
     @width.setter
     def width(self, width: int):
@@ -418,7 +416,7 @@ def width(self, width: int):
         width : int
             The width of the image in pixels.
         """
-        self.cam.prop_setvalue(4202784, width)  # TODO: find DCAM keyword for this
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYHSIZE, width)
 
     @property
     def height(self):
@@ -432,7 +430,7 @@ def height(self):
         int:
             The height of the image in pixels.
         """
-        return self.cam.prop_getvalue(4202816)  # TODO: find DCAM keyword for this
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.SUBARRAYVSIZE)
 
     @height.setter
     def height(self, height: int):
@@ -446,7 +444,7 @@ def height(self, height: int):
         height : int
             The height of the image in pixels.
         """
-        self.cam.prop_setvalue(4202816, height)  # TODO: find DCAM keyword for this
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYVSIZE, height)
 
     @property
     def offset_x(self):
@@ -460,7 +458,7 @@ def offset_x(self):
         int:
             The x offset of the image in pixels.
         """
-        return self.cam.prop_getvalue(4202800)  # TODO: find DCAM keyword for this
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.SUBARRAYVPOS)
 
     @offset_x.setter
     def offset_x(self, offset_x: int):
@@ -474,7 +472,7 @@ def offset_x(self, offset_x: int):
         offset_x : int
             The x offset of the image in pixels.
         """
-        self.cam.prop_setvalue(4202800, offset_x)  # TODO: find DCAM keyword for this
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYVPOS, offset_x)
 
     @property
     def offset_y(self):
@@ -488,7 +486,7 @@ def offset_y(self):
         int:
             The y offset of the image in pixels.
         """
-        return self.cam.prop_getvalue(4202768)  # TODO: find DCAM keyword for this
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.SUBARRAYHPOS)
 
     @offset_y.setter
     def offset_y(self, offset_y: int):
@@ -502,7 +500,7 @@ def offset_y(self, offset_y: int):
         offset_y : int
             The y offset of the image in pixels.
         """
-        self.cam.prop_setvalue(4202768, offset_x)  # TODO: find DCAM keyword for this
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYHPOS, offset_y)
 
 
 if __name__ == '__main__':

From 42ec86d87719d2d6cc9752b432724f2753c95d75 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Wed, 17 Apr 2024 22:27:11 +0200
Subject: [PATCH 07/25] Add comment

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 992e9f57e..00738c385 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -103,6 +103,8 @@ def open(self):
         ------
         ValueError
             If the pixel format is invalid.
+        RuntimeError
+            For a Dcamapi or Dcam error when initializing the library or when opening the camera.
         """
         if dcam.Dcamapi.init() is False:
             raise RuntimeError(f'Dcamapi.init() fails with error {dcam.Dcamapi.lasterr()}')

From 5614629282cb85cadb40ae1bf19e307bac2a671b Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Wed, 17 Apr 2024 22:42:56 +0200
Subject: [PATCH 08/25] Code sneak: remove property device_name from AV cam
 since unused

---
 catkit2/services/allied_vision_camera/allied_vision_camera.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/catkit2/services/allied_vision_camera/allied_vision_camera.py b/catkit2/services/allied_vision_camera/allied_vision_camera.py
index d2856adcb..2d529e593 100644
--- a/catkit2/services/allied_vision_camera/allied_vision_camera.py
+++ b/catkit2/services/allied_vision_camera/allied_vision_camera.py
@@ -243,8 +243,6 @@ def make_property_helper(name, read_only=False):
         make_property_helper('sensor_width', read_only=True)
         make_property_helper('sensor_height', read_only=True)
 
-        make_property_helper('device_name', read_only=True)
-
         self.make_command('start_acquisition', self.start_acquisition)
         self.make_command('end_acquisition', self.end_acquisition)
 

From 529d17731851599d63dda83238385e620cab2ef5 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Wed, 17 Apr 2024 22:43:23 +0200
Subject: [PATCH 09/25] Simplify docstrings

---
 .../hamamatsu_camera/hamamatsu_camera.py      | 25 -------------------
 1 file changed, 25 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 00738c385..fa6d98e07 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -48,25 +48,6 @@ class HamamatsuCamera(Service):
         An event to signal whether the camera should be acquiring images.
     NUM_FRAMES : int
         The number of frames to allocate for the data streams.
-
-    Methods
-    -------
-    open()
-        Open the service.
-    main()
-        The main function of the service.
-    close()
-        Close the service.
-    acquisition_loop()
-        The main acquisition loop.
-    monitor_temperature()
-        Monitor the temperature of the camera.
-    start_acquisition()
-        Start the acquisition loop.
-    end_acquisition()
-        End the acquisition loop.
-    get_temperature()
-        Get the temperature of the camera.
     """
     NUM_FRAMES = 20
 
@@ -192,12 +173,6 @@ def main(self):
                 self.acquisition_loop()
 
     def close(self):
-        """
-        Close the service.
-
-        This function is called when the service is closed.
-        It stops the acquisition loop and cleans up the camera and data streams.
-        """
         self.cam.dev_close()
         self.cam = None
 

From 77935e8171bff442084dc0076b9d369e6eef743b Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Wed, 17 Apr 2024 22:43:37 +0200
Subject: [PATCH 10/25] Some cleaning

---
 .../hamamatsu_camera/hamamatsu_camera.py      | 24 ++++++++-----------
 1 file changed, 10 insertions(+), 14 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index fa6d98e07..d09a9c1e2 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -100,17 +100,15 @@ def open(self):
         self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYMODE, 2.0)  # TODO: ? - 2.0 for subarray mode on
 
         # Set binning
-        self.cam.prop_setvalue(dcam.DCAM_IDPROP.BINNING, 1.0)  # TODO: read from config
+        binning = self.config.get('binning', 1)
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.BINNING, binning)
 
-        # Set camera mode
-        dcam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, 2.0)   # TODO: read from config - 2.0 for "standard", 1.0 for "ultraquiet"
+        # Set camera mode to "ultraquiet" (1.0) rather than "standard" (2.0)
+        dcam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, 1.0)
 
         self.current_pixel_format = self.config.get('pixel_format', 'Mono16')
         if self.current_pixel_format not in self.pixel_formats:
-            raise ValueError('Invalid pixel format: ' +
-                             self.current_pixel_format +
-                             ', must be one of ' +
-                             str(list(self.pixel_formats.keys())))
+            raise ValueError(f'Invalid pixel format: {self.current_pixel_format}, must be one of {str(list(self.pixel_formats.keys()))}')
         self.log.info('Using pixel format: %s', self.current_pixel_format)
         self.cam.prop_setvalue(dcam.DCAM_IDPROP.IMAGE_PIXELTYPE, self.pixel_formats[self.current_pixel_format])
 
@@ -153,8 +151,6 @@ def make_property_helper(name, read_only=False):
         make_property_helper('sensor_width', read_only=True)
         make_property_helper('sensor_height', read_only=True)
 
-        make_property_helper('device_name', read_only=True)
-
         self.make_command('start_acquisition', self.start_acquisition)
         self.make_command('end_acquisition', self.end_acquisition)
 
@@ -203,7 +199,7 @@ def acquisition_loop(self):
                 if self.cam.lasterr().is_timeout():
                     self.log.warning('Timeout while waiting for frame')
                 if self.cam.wait_capevent_frameready(timeout_millisec) is False:
-                    raise RuntimeError(f'Dcam.wait_capevent_frameready() fails with error {self.cam.lasterr()}')
+                    raise RuntimeError(f'Dcam.wait_capevent_frameready({timeout_millisec}) fails with error {self.cam.lasterr()}')
                 img = self.cam.buf_getlastframedata()
                 self.images.submit_data(img)
 
@@ -295,7 +291,7 @@ def gain(self):
         int:
             The gain of the camera.
         """
-        return self.cam.Gain.get()   # TODO
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.CONTRASTGAIN)   # TODO: verify this
 
     @gain.setter
     def gain(self, gain: int):
@@ -309,7 +305,7 @@ def gain(self, gain: int):
         gain : int
             The gain of the camera.
         """
-        self.cam.Gain.set(gain)   # TODO
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.CONTRASTGAIN, gain)   # TODO: verify this
 
     @property
     def brightness(self):
@@ -323,7 +319,7 @@ def brightness(self):
         int:
             The brightness of the camera.
         """
-        return self.cam.Brightness.get()   # TODO
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.XXX)   # TODO: find correct property
 
     @brightness.setter
     def brightness(self, brightness: int):
@@ -337,7 +333,7 @@ def brightness(self, brightness: int):
         brightness : int
             The brightness of the camera.
         """
-        self.cam.Brightness.set(brightness)   # TODO
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.XXX, brightness)   # TODO: find correct property
 
     @property
     def sensor_width(self):

From bee35d51b190950a54fc9186fe901f1361e8044b Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 18 Apr 2024 13:15:56 +0200
Subject: [PATCH 11/25] Fix typo in pixel type

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index d09a9c1e2..d6291ecef 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -61,8 +61,8 @@ def __init__(self):
 
         # Dictionary to store the pixel format and the corresponding numpy dtype and dcam pixel format
         self.pixel_formats = {
-            "Mono8": dcam.DCAM_PIXELTYPE.Mono8,
-            "Mono16": dcam.DCAM_PIXELTYPE.Mono16,
+            "Mono8": dcam.DCAM_PIXELTYPE.MONO8,
+            "Mono16": dcam.DCAM_PIXELTYPE.MONO16,
         }
         self.current_pixel_format = None
         self.temperature_thread = None

From f930523a35bc9d9d95fb47053585a44b1b5fc3a0 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 18 Apr 2024 13:24:03 +0200
Subject: [PATCH 12/25] Call prop_setvalue() on camera, not on library

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index d6291ecef..66234c186 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -104,7 +104,7 @@ def open(self):
         self.cam.prop_setvalue(dcam.DCAM_IDPROP.BINNING, binning)
 
         # Set camera mode to "ultraquiet" (1.0) rather than "standard" (2.0)
-        dcam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, 1.0)
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, 1.0)
 
         self.current_pixel_format = self.config.get('pixel_format', 'Mono16')
         if self.current_pixel_format not in self.pixel_formats:

From a204ee94b66848ea66077e14e2613779b2a3552b Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 18 Apr 2024 13:33:54 +0200
Subject: [PATCH 13/25] Return sensor width and height as int

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 66234c186..9f8b434e6 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -347,7 +347,7 @@ def sensor_width(self):
         int:
             The width of the sensor in pixels.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_WIDTH)
+        return int(self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_WIDTH))
 
     @property
     def sensor_height(self):
@@ -361,7 +361,7 @@ def sensor_height(self):
         int:
             The height of the sensor in pixels.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_HEIGHT)
+        return int(self.cam.prop_getvalue(dcam.DCAM_IDPROP.IMAGE_HEIGHT))
 
     @property
     def width(self):

From 527d1f93d3bf5c8582097c1e502f371df2089875 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 18 Apr 2024 13:40:23 +0200
Subject: [PATCH 14/25] Define image dtype before submitting to data stream

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 9f8b434e6..8b3e6b392 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -201,7 +201,7 @@ def acquisition_loop(self):
                 if self.cam.wait_capevent_frameready(timeout_millisec) is False:
                     raise RuntimeError(f'Dcam.wait_capevent_frameready({timeout_millisec}) fails with error {self.cam.lasterr()}')
                 img = self.cam.buf_getlastframedata()
-                self.images.submit_data(img)
+                self.images.submit_data(img.astype('float32'))
 
         finally:
             # Stop acquisition.

From a734a0a40cc9de5fbbca632cff6471b3b623a2b5 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 18 Apr 2024 13:40:51 +0200
Subject: [PATCH 15/25] Return ROI width and height as int

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 8b3e6b392..f20465e5d 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -375,7 +375,7 @@ def width(self):
         int:
             The width of the image in pixels.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.SUBARRAYHSIZE)
+        return int(self.cam.prop_getvalue(dcam.DCAM_IDPROP.SUBARRAYHSIZE))
 
     @width.setter
     def width(self, width: int):
@@ -403,7 +403,7 @@ def height(self):
         int:
             The height of the image in pixels.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.SUBARRAYVSIZE)
+        return int(self.cam.prop_getvalue(dcam.DCAM_IDPROP.SUBARRAYVSIZE))
 
     @height.setter
     def height(self, height: int):

From fb4c4424fbd0a0410c2d01558c27a160686713f4 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 18 Apr 2024 13:46:29 +0200
Subject: [PATCH 16/25] Stick in SENSITIVITY keyword for brightness

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index f20465e5d..5e6fbccdd 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -291,7 +291,7 @@ def gain(self):
         int:
             The gain of the camera.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.CONTRASTGAIN)   # TODO: verify this
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.CONTRASTGAIN)
 
     @gain.setter
     def gain(self, gain: int):
@@ -305,7 +305,7 @@ def gain(self, gain: int):
         gain : int
             The gain of the camera.
         """
-        self.cam.prop_setvalue(dcam.DCAM_IDPROP.CONTRASTGAIN, gain)   # TODO: verify this
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.CONTRASTGAIN, gain)
 
     @property
     def brightness(self):
@@ -319,7 +319,7 @@ def brightness(self):
         int:
             The brightness of the camera.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.XXX)   # TODO: find correct property
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.SENSITIVITY)
 
     @brightness.setter
     def brightness(self, brightness: int):
@@ -333,7 +333,7 @@ def brightness(self, brightness: int):
         brightness : int
             The brightness of the camera.
         """
-        self.cam.prop_setvalue(dcam.DCAM_IDPROP.XXX, brightness)   # TODO: find correct property
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.SENSITIVITY, brightness)
 
     @property
     def sensor_width(self):

From d2f978f81dbd455ac518f42c831178b7dfa37c94 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 18 Apr 2024 13:52:28 +0200
Subject: [PATCH 17/25] Clarify subarray mode setting

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 5e6fbccdd..f35615777 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -96,8 +96,8 @@ def open(self):
         if self.cam.dev_open() is False:
             raise RuntimeError(f'Dcam.dev_open() fails with error {self.cam.lasterr()}')
 
-        # Set subarray mode
-        self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYMODE, 2.0)  # TODO: ? - 2.0 for subarray mode on
+        # Set subarray mode to on so that it checks subarray compatibility when picking ROI
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYMODE, 2.0)
 
         # Set binning
         binning = self.config.get('binning', 1)

From c2b7356a42e3b19737c72be3e4e117df6f3ddb8e Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 18 Apr 2024 14:08:59 +0200
Subject: [PATCH 18/25] Read camera mode from config

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index f35615777..a817ce004 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -103,8 +103,15 @@ def open(self):
         binning = self.config.get('binning', 1)
         self.cam.prop_setvalue(dcam.DCAM_IDPROP.BINNING, binning)
 
-        # Set camera mode to "ultraquiet" (1.0) rather than "standard" (2.0)
-        self.cam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, 1.0)
+        # Set camera mode
+        camera_mode = self.config.get('camera_mode', "standard")
+        if camera_mode == "ultraquiet":
+            self.camera_mode = 1.0
+        elif camera_mode == "standard":
+            self.camera_mode = 2.0
+        else:
+            raise ValueError(f'Invalid camera mode: {camera_mode}, must be one of ["ultraquiet", "standard"]')
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, self.camera_mode)
 
         self.current_pixel_format = self.config.get('pixel_format', 'Mono16')
         if self.current_pixel_format not in self.pixel_formats:

From a9199a2b0d35ef1189e3ed2ec2c9fc6e2d77da34 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Mon, 22 Apr 2024 14:35:11 +0200
Subject: [PATCH 19/25] Drop first frame in acquisition loop

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index a817ce004..b9714f7a5 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -207,6 +207,12 @@ def acquisition_loop(self):
                     self.log.warning('Timeout while waiting for frame')
                 if self.cam.wait_capevent_frameready(timeout_millisec) is False:
                     raise RuntimeError(f'Dcam.wait_capevent_frameready({timeout_millisec}) fails with error {self.cam.lasterr()}')
+
+                if self.cam.buf_getframedata(-2) is False:
+                    # If there is no second to last frame, it means we just acquired the first frame.
+                    # In this case, drop the current frame since it always contains systematic errors.
+                    continue
+
                 img = self.cam.buf_getlastframedata()
                 self.images.submit_data(img.astype('float32'))
 

From 8f3307f1cea23e91e2dedf433bb5c90bcf5c93ed Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Mon, 22 Apr 2024 23:14:47 +0200
Subject: [PATCH 20/25] Add log message when dropping first frame

---
 catkit2/services/hamamatsu_camera/hamamatsu_camera.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index b9714f7a5..8d27f6268 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -211,6 +211,7 @@ def acquisition_loop(self):
                 if self.cam.buf_getframedata(-2) is False:
                     # If there is no second to last frame, it means we just acquired the first frame.
                     # In this case, drop the current frame since it always contains systematic errors.
+                    self.log.info('Dropping first camera frame')
                     continue
 
                 img = self.cam.buf_getlastframedata()

From ae3448378b071030dd6474f1aca1682c196f5b0d Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Mon, 22 Apr 2024 23:20:51 +0200
Subject: [PATCH 21/25] Handle exposure time in microseconds

---
 .../services/hamamatsu_camera/hamamatsu_camera.py  | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 8d27f6268..8247d603d 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -129,7 +129,7 @@ def open(self):
         self.offset_y = offset_y
 
         self.gain = self.config.get('gain', 0)
-        self.exposure_time = self.config.get('exposure_time', 1)
+        self.exposure_time = self.config.get('exposure_time', 1000)
         self.temperature = self.make_data_stream('temperature', 'float64', [1], 20)
 
         # Create datastreams
@@ -268,30 +268,30 @@ def get_temperature(self):
     @property
     def exposure_time(self):
         """
-        The exposure time in seconds.
+        The exposure time in microseconds.
 
         This property can be used to get the exposure time of the camera.
 
         Returns:
         --------
         float:
-            The exposure time in seconds.
+            The exposure time in microseconds.
         """
-        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.EXPOSURETIME)
+        return self.cam.prop_getvalue(dcam.DCAM_IDPROP.EXPOSURETIME) * 1e6
 
     @exposure_time.setter
     def exposure_time(self, exposure_time: float):
         """
-        Set the exposure time in seconds.
+        Set the exposure time in microseconds.
 
         This property can be used to set the exposure time of the camera.
 
         Parameters
         ----------
         exposure_time : float
-            The exposure time in seconds.
+            The exposure time in microseconds.
         """
-        self.cam.prop_setvalue(dcam.DCAM_IDPROP.EXPOSURETIME, exposure_time)
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.EXPOSURETIME, exposure_time / 1e6)
 
     @property
     def gain(self):

From 243b5ca553f1c14e510f46f074465bad7e7307d1 Mon Sep 17 00:00:00 2001
From: THD2-team <thd2team@gmail.com>
Date: Wed, 24 Apr 2024 10:54:12 +0200
Subject: [PATCH 22/25] Fix first frame dropping

---
 .../services/hamamatsu_camera/hamamatsu_camera.py    | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index 8247d603d..a7b33b8b3 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -202,21 +202,25 @@ def acquisition_loop(self):
 
         timeout_millisec = 2000
         try:
+            i = 0
             while self.should_be_acquiring.is_set() and not self.should_shut_down:
                 if self.cam.lasterr().is_timeout():
                     self.log.warning('Timeout while waiting for frame')
                 if self.cam.wait_capevent_frameready(timeout_millisec) is False:
                     raise RuntimeError(f'Dcam.wait_capevent_frameready({timeout_millisec}) fails with error {self.cam.lasterr()}')
 
-                if self.cam.buf_getframedata(-2) is False:
-                    # If there is no second to last frame, it means we just acquired the first frame.
-                    # In this case, drop the current frame since it always contains systematic errors.
+                img = self.cam.buf_getlastframedata()
+
+                if i == 0:
+                    # The first frame often contains systematic errors, so drop it.
                     self.log.info('Dropping first camera frame')
+                    i += 1
                     continue
 
-                img = self.cam.buf_getlastframedata()
                 self.images.submit_data(img.astype('float32'))
 
+                i += 1
+
         finally:
             # Stop acquisition.
             self.cam.cap_stop()

From 568bf8f99dc7e8cfcc9dacdb6cfef2c64f48aae1 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Fri, 26 Apr 2024 14:18:24 +0200
Subject: [PATCH 23/25] Add a service doc for the Hamamatsu camera

---
 docs/services/hamamatsu_camera.rst | 69 ++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 docs/services/hamamatsu_camera.rst

diff --git a/docs/services/hamamatsu_camera.rst b/docs/services/hamamatsu_camera.rst
new file mode 100644
index 000000000..3de65e414
--- /dev/null
+++ b/docs/services/hamamatsu_camera.rst
@@ -0,0 +1,69 @@
+Hamamatsu Camera
+====================
+
+This service controls a Hamamatsu camera. It is a wrapper around the DCAM SDK, which is distributed on the manufacturer
+website together with their Python API ``dcam``: `https://www.hamamatsu.com/eu/en/product/cameras/software/driver-software.html <https://www.hamamatsu.com/eu/en/product/cameras/software/driver-software.html>`_
+
+The service requires the definition of an environment variable ``CATKIT_DCAM_SDK_PATH`` that points to the
+``python`` directory within the DCAM SDK installation.
+
+The service has been successfully tested with the following camera models:
+- Hamamatsu ORCA-Quest C15550-20UP
+
+Configuration
+-------------
+
+.. code-block:: YAML
+
+    camera1:
+      service_type: hamamatsu_camera
+      simulated_service_type: camera_sim
+      requires_safety: false
+
+      camera_id: 0
+      camera_mode: 'ultraquiet'
+      pixel_format: Mono16
+      binning: 1
+
+      offset_x: 0
+      offset_y: 0
+      width: 400
+      height: 400
+      sensor_width: 4096
+      sensor_height: 2304
+      exposure_time: 8294.4
+      gain: 0
+
+Properties
+----------
+``exposure_time``: Exposure time of the camera.
+
+``gain``: Gain of the camera.
+
+``brightness``: Brightness of the camera.
+
+``width``: The width of the camera.
+
+``height``: The height of the camera.
+
+``offset_x``: The x offset of the camera.
+
+``offset_y``: The y offset of the camera.
+
+``sensor_width``: The width of the sensor.
+
+``sensor_height``: The height of the sensor.
+
+Commands
+--------
+``start_acquisition()``: This starts the acquisition of images from the camera.
+
+``end_acquisition()``: This ends the acquisition of images from the camera.
+
+Datastreams
+-----------
+``temperature``: The temperature as measured by this sensor in Celsius.
+
+``images``: The images acquired by the camera.
+
+``is_acquiring``: Whether the camera is currently acquiring images.
\ No newline at end of file

From 028928dca3099ac1c00839cb692973a0fc050dac Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Fri, 26 Apr 2024 15:13:36 +0200
Subject: [PATCH 24/25] Specify exposure time units

---
 docs/services/allied_vision_camera.rst | 2 +-
 docs/services/hamamatsu_camera.rst     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/services/allied_vision_camera.rst b/docs/services/allied_vision_camera.rst
index 2d81800f3..cf2b32d3e 100644
--- a/docs/services/allied_vision_camera.rst
+++ b/docs/services/allied_vision_camera.rst
@@ -41,7 +41,7 @@ Configuration
 
 Properties
 ----------
-``exposure_time``: Exposure time of the camera.
+``exposure_time``: Exposure time of the camera in microseconds.
 
 ``gain``: Gain of the camera.
 
diff --git a/docs/services/hamamatsu_camera.rst b/docs/services/hamamatsu_camera.rst
index 3de65e414..507535984 100644
--- a/docs/services/hamamatsu_camera.rst
+++ b/docs/services/hamamatsu_camera.rst
@@ -36,7 +36,7 @@ Configuration
 
 Properties
 ----------
-``exposure_time``: Exposure time of the camera.
+``exposure_time``: Exposure time of the camera in microseconds.
 
 ``gain``: Gain of the camera.
 

From d7edf0fe9d88f3273697c93e87d2ea29d09f7f99 Mon Sep 17 00:00:00 2001
From: Iva Laginja <iva.laginja@obspm.fr>
Date: Thu, 23 May 2024 14:43:55 +0200
Subject: [PATCH 25/25] Add setting of detector- and hot pixel correction modes
 from config

---
 .../hamamatsu_camera/hamamatsu_camera.py      | 30 +++++++++++++------
 1 file changed, 21 insertions(+), 9 deletions(-)

diff --git a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
index a7b33b8b3..b77f8b69c 100644
--- a/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
+++ b/catkit2/services/hamamatsu_camera/hamamatsu_camera.py
@@ -99,19 +99,31 @@ def open(self):
         # Set subarray mode to on so that it checks subarray compatibility when picking ROI
         self.cam.prop_setvalue(dcam.DCAM_IDPROP.SUBARRAYMODE, 2.0)
 
-        # Set binning
         binning = self.config.get('binning', 1)
         self.cam.prop_setvalue(dcam.DCAM_IDPROP.BINNING, binning)
 
-        # Set camera mode
-        camera_mode = self.config.get('camera_mode', "standard")
-        if camera_mode == "ultraquiet":
-            self.camera_mode = 1.0
-        elif camera_mode == "standard":
-            self.camera_mode = 2.0
+        detector_correction = 2.0 if self.config.get('detector_correction', True) else 1.0
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.DEFECTCORRECT_MODE, detector_correction)
+
+        self.hot_pixel_correction = self.config.get('hot_pixel_correction', 'standard')
+        if self.hot_pixel_correction == "standard":
+            hot_pixel_correction = 1.0
+        elif self.hot_pixel_correction == "minimum":
+            hot_pixel_correction = 2.0
+        elif self.hot_pixel_correction == "aggressive":
+            hot_pixel_correction = 3.0
+        else:
+            raise ValueError(f'Invalid hot pixel correction: {self.hot_pixel_correction}, must be one of ["standard", "minimum", "aggressive"]')
+        self.cam.prop_setvalue(self.cam.DCAM_IDPROP.HOTPIXELCORRECT_LEVEL, hot_pixel_correction)
+
+        self.camera_mode = self.config.get('camera_mode', "standard")
+        if self.camera_mode == "ultraquiet":
+            camera_mode = 1.0
+        elif self.camera_mode == "standard":
+            camera_mode = 2.0
         else:
-            raise ValueError(f'Invalid camera mode: {camera_mode}, must be one of ["ultraquiet", "standard"]')
-        self.cam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, self.camera_mode)
+            raise ValueError(f'Invalid camera mode: {self.camera_mode}, must be one of ["ultraquiet", "standard"]')
+        self.cam.prop_setvalue(dcam.DCAM_IDPROP.READOUTSPEED, camera_mode)
 
         self.current_pixel_format = self.config.get('pixel_format', 'Mono16')
         if self.current_pixel_format not in self.pixel_formats: