Merge pull request #294 from TheDeanLab/initial_stage_position

Initial stage position

Author: AdvancedImagingUTSW

src/aslm/config/configuration.yaml

@@ -132,10 +132,7 @@ microscopes:
         type: PI
         serial_number: 119060508
         axes: [x, y, z, theta, f]
-      y_unload_position: 10000
-      y_load_position: 90000
 
-      startfocus: 75000
       x_max: 33500
       x_min: 16000
       y_max: 100000
@@ -147,29 +144,13 @@ microscopes:
       theta_max: 360
       theta_min: 0
 
-      x_rot_position: 2000
-      y_rot_position: 2000
-      z_rot_position: 2000
-
       x_step: 500
       y_step: 500
       z_step: 500
       theta_step: 30
       f_step: 500
-
-      position:
-        x_pos: 25250
-        y_pos: 40000
-        z_pos: 40000
-        f_pos: 70000
-        theta_pos: 0
       velocity: 1000
 
-      x_offset: 0
-      y_offset: 0
-      z_offset: 0
-      f_offset: 0
-      theta_offset: 0
     zoom:
       hardware:
         name: zoom
@@ -360,10 +341,7 @@ microscopes:
           type: Thorlabs
           serial_number: 74000375
           axes: [f]
-      y_unload_position: 10000
-      y_load_position: 90000
 
-      startfocus: 75000
       x_max: 33500
       x_min: 16000
       y_max: 100000
@@ -375,29 +353,13 @@ microscopes:
       theta_max: 360
       theta_min: 0
 
-      x_rot_position: 2000
-      y_rot_position: 2000
-      z_rot_position: 2000
-
       x_step: 500
       y_step: 500
       z_step: 500
       theta_step: 30
       f_step: 500
-
-      position:
-        x_pos: 25250
-        y_pos: 40000
-        z_pos: 40000
-        f_pos: 0
-        theta_pos: 0
       velocity: 1000
 
-      x_offset: 1500
-      y_offset: 1720
-      z_offset: -14311
-      f_offset: 0
-      theta_offset: 0
     zoom:
       position:
         N/A: 0

src/aslm/model/device_startup_functions.py

@@ -129,7 +129,7 @@ def load_camera_connection(configuration,
         # Locally Import Hamamatsu API and Initialize Camera Controller
         HamamatsuController = importlib.import_module('aslm.model.devices.APIs.hamamatsu.HamamatsuAPI')
         return auto_redial(HamamatsuController.DCAM, (camera_id,), exception=Exception)
-    elif cam_type.lower() == 'syntheticcamera' or device_type.lower() == 'synthetic':
+    elif cam_type.lower() == 'syntheticcamera' or cam_type.lower() == 'synthetic':
         from aslm.model.devices.camera.camera_synthetic import SyntheticCameraController
         return SyntheticCameraController()
     else:
@@ -169,7 +169,7 @@ def start_camera(microscope_name,
     if cam_type == 'HamamatsuOrca':
         from aslm.model.devices.camera.camera_hamamatsu import HamamatsuOrca
         return HamamatsuOrca(microscope_name, device_connection, configuration)
-    elif cam_type.lower() == 'syntheticcamera' or device_type.lower() == 'synthetic':
+    elif cam_type.lower() == 'syntheticcamera' or cam_type.lower() == 'synthetic':
         from aslm.model.devices.camera.camera_synthetic import SyntheticCamera
         return SyntheticCamera(microscope_name, device_connection, configuration)
     else:

src/aslm/model/devices/camera/camera_synthetic.py

@@ -266,4 +266,19 @@ def get_minimum_waiting_time(self):
         """
         return 0.01
 
+    def calculate_readout_time(self):
+        r""" Calculate duration of time needed to readout an image.
+        Calculates the readout time and maximum frame rate according to the camera configuration settings.
 
+        Returns
+        -------
+        readout_time : float
+            Duration of time needed to readout an image.
+        max_frame_rate : float
+            Maximum framerate for a given camera acquisition mode.
+
+        """
+        exposure_time = self.camera_controller.get_property_value('exposure_time')
+        readout_time = 0.01  # 10 milliseconds.
+        max_frame_rate = 1 / (exposure_time + readout_time)
+        return readout_time, max_frame_rate