HW: PyVCAM adapter

copylot/gui/_qt/dockables/camera.py

@@ -0,0 +1,36 @@
+from qtpy.QtCore import Qt
+from qtpy.QtWidgets import (
+    QWidget,
+    QHBoxLayout,
+    QGridLayout,
+    QLabel,
+    QLineEdit,
+)
+
+
+class CameraDockWidget(QWidget):
+    def __init__(self, parent):
+        super(QWidget, self).__init__(parent)
+        self.parent = parent
+
+        self.main_layout = QHBoxLayout()
+
+        self.parameters_layout = QGridLayout()
+        row_index = 0
+        parameter_label = QLabel("Exposure duration:", self)
+        parameter_editbox = QLineEdit(str(0.01), self)
+
+        self.parameters_layout.addWidget(
+            parameter_label, row_index, 0, alignment=Qt.AlignTop
+        )
+        self.parameters_layout.addWidget(
+            parameter_editbox, row_index, 1, alignment=Qt.AlignTop
+        )
+
+        self.main_layout.addLayout(self.parameters_layout)
+
+        self.setLayout(self.main_layout)
+
+    @property
+    def parameters(self):
+        raise NotImplementedError("camera.parameters not yet implemented")

copylot/gui/gui.py

@@ -114,6 +114,10 @@ def __init__(self, *args, **kwargs):
         self.laser_dock.setTitleBarWidget(QLabel("Laser"))
         self.dock_list.append(self.laser_dock)
 
+        self.camera_dock = QDockWidget(self)
+        self.camera_dock.setTitleBarWidget(QLabel("Camera"))
+        self.dock_list.append(self.camera_dock)
+
         for dock in self.dock_list:
             _apply_dock_config(dock)
 
@@ -144,6 +148,10 @@ def __init__(self, *args, **kwargs):
             DockPlaceholder(self, self.laser_dock, "laser", [self])
         )
 
+        self.camera_dock.setWidget(
+            DockPlaceholder(self, self.camera_dock, "camera", [self])
+        )
+
         # self.parameters_widget = ParametersDockWidget(self)
         self.parameters_placeholder = DockPlaceholder(
             self, self.parameters_dock, "parameters", [self]
@@ -156,6 +164,7 @@ def __init__(self, *args, **kwargs):
         self.splitDockWidget(self.live_dock, self.timelapse_dock, Qt.Vertical)
         self.splitDockWidget(self.timelapse_dock, self.water_dock, Qt.Vertical)
         self.splitDockWidget(self.water_dock, self.laser_dock, Qt.Vertical)
+        self.splitDockWidget(self.laser_dock, self.camera_dock, Qt.Vertical)
 
         # create status bar that is updated from live and timelapse control classes
         self.status_bar = QStatusBar()

copylot/hardware/prime_bsi_camera/camera.py

@@ -0,0 +1,182 @@
+from pyvcam import pvc, constants
+from pyvcam.camera import Camera
+
+
+class PrimeBSICamera:
+    def __init__(
+        self,
+        camera_name: str = None,
+        # TODO: create properties for these
+        # scan_mode: str = None,
+        # scan_dir: str = None,
+        # binning: tuple = (1, 1),
+        # trigger_mode: str = None,
+        # exposure_out: str = None,
+        enable_metadata: bool = True,
+    ):
+        """
+
+        Parameters
+        ----------
+        camera_name : str
+            Camera name, available through available_cameras().
+            If not provided, the next available camera will be initialized.
+        enable_metadata : bool
+            Toggles camera metadata on and off. By default, it is True.
+        """
+        pvc.init_pvcam()
+
+        try:
+            if camera_name:
+                self.cam = Camera.select_camera(camera_name)
+            else:
+                self.cam = next(Camera.detect_camera())
+        except:
+            pvc.uninit_pvcam()
+            raise
+
+        self.cam.open()
+
+        # Prime BSI Express camera has only one port called 'CMOS' at index 0
+        self.cam.readout_port = 0
+
+        # Hard-coding these values since they won't change
+        # Values can be parsed from self.cam.port_speed_gain_table['CMOS']
+        self._speed_gain_table = {'200 MHz': {'speed_index': 0,
+                                              'Full well': {'gain_index': 1, 'bit_depth': 11},
+                                              'Balanced': {'gain_index': 2, 'bit_depth': 11},
+                                              'Sensitivity': {'gain_index': 3, 'bit_depth': 11}
+                                              },
+                                  '100 MHz': {'speed_index': 1,
+                                              'HDR': {'gain_index': 1, 'bit_depth': 16},
+                                              'CMS': {'gain_index': 2, 'bit_depth': 12}
+                                              }
+                                  }
+
+        self.serial_number = self.cam.serial_no
+        self.sensor_size = self.cam.sensor_size
+        self.chip_name = self.cam.chip_name
+        self.cam.meta_data_enabled = enable_metadata
+
+    def __del__(self):
+        self.cam.finish()
+        self.cam.close()
+        pvc.uninit_pvcam()
+
+    @staticmethod
+    def available_cameras():
+        pvc.init_pvcam()
+        cameras = Camera.get_available_camera_names()
+
+        pvc.uninit_pvcam()
+        return cameras
+
+    @property
+    def speed_gain_table(self):
+        return self._speed_gain_table
+
+    # Will implement later
+    # def available_scan_modes(self):
+    #     scan_modes = self.cam.__prog_scan_modes
+    #
+    #     print(f"Available scan modes: {scan_modes}")
+    #
+    #     return scan_modes
+
+    @property
+    def exposure_time(self):
+        return self.cam.exp_time
+
+    @exposure_time.setter
+    def exposure_time(self, exposure_time):
+        self.cam.exp_time = exposure_time
+
+    @property
+    def readout_speed(self):
+        readout_speed_name = None
+
+        readout_speed_index = self.cam.speed_table_index
+        for key, value in self.speed_gain_table.items():
+            if value['speed_index'] == readout_speed_index:
+                readout_speed_name = key
+
+        return readout_speed_name
+
+    @readout_speed.setter
+    def readout_speed(self, new_speed):
+        success = False
+
+        for key, value in self.speed_gain_table.items():
+            if key == new_speed:
+                success = True
+                self.cam.speed_table_index = value['speed_index']
+
+        if not success:
+            raise ValueError('Invalid readout speed. '
+                             'Please check speed_gain_table for valid settings.')
+
+    @property
+    def gain(self):
+        gain_name = None
+
+        for key, value in self.speed_gain_table[self.readout_speed].items():
+            if isinstance(value, dict):
+                if value['gain_index'] == self.cam.gain:
+                    gain_name = key
+
+        return gain_name
+
+    @gain.setter
+    def gain(self, gain):
+        success = False
+
+        for key, value in self.speed_gain_table[self.readout_speed].items():
+            if key == gain:
+                success = True
+                self.cam.gain = value['gain_index']
+
+        if not success:
+            raise ValueError('Invalid gain. '
+                             'Please check speed_gain_table for valid settings.')
+
+    @property
+    def bit_depth(self):
+        return self.speed_gain_table[self.readout_speed][self.gain]['bit_depth']
+
+    def reset_rois(self):
+        """Restores ROI to the default."""
+        self.cam.reset_rois()
+
+    def set_roi(self, s1: int, p1: int, width: int, height: int):
+        """
+        Adds a new ROI with given parameters to the list of ROIs.
+
+        Parameters
+        ----------
+        s1 : int
+            Serial coordinate of the first corner
+        p1 : int
+            Parallel coordinate of the first corner
+        width : int
+            Width of ROI in number of pixels
+        height : int
+            Height of ROI in number of pixels
+
+        """
+        self.cam.set_roi(s1, p1, width, height)
+
+    def live_run(self, exposure: int = 20):
+        """
+        Live mode run method.
+
+        Parameters
+        ----------
+        exposure : int
+
+        Returns
+        -------
+
+        """
+        self.cam.start_live(exposure)
+
+        return self.cam.poll_frame

copylot/microscope_config/configs/mantis.yaml

@@ -2,3 +2,11 @@ name: mantis
 hardware:
   - ni_daq:
       show_gui: true
+  - prime_bsi_camera:
+      TRIGGER_MODE: "NORMAL"
+      TRIGGERPOLARITY: "POSITIVE"
+      TRIGGER_CONNECTOR: "BNC"
+      TRIGGERTIMES: 1
+      TRIGGERDELAY: 0
+      TRIGGERSOURCE: "EXTERNAL"
+      TRIGGERACTIVE: "SYNCREADOUT"