Fix silent calibration failures

recOrder/plugin/workers/calibration_workers.py

@@ -223,6 +223,8 @@ def _calibrate_4state(self):
  Run through the 4-state calibration algorithm
  """
 
+ search_radius = np.min((self.calib.swing/self.calib.ratio, 0.05))
+
  self.calib.calib_scheme = '4-State'
 
  self._check_abort()
@@ -240,19 +242,21 @@ def _calibrate_4state(self):
  self._check_abort()
 
  # Optimize 60 deg state
- self.calib.opt_I60(0.05, 0.05)
+ self.calib.opt_I60(search_radius, search_radius)
  self.progress_update.emit((75, 'Calibrating State 3...'))
 
  self._check_abort()
 
  # Optimize 120 deg state
- self.calib.opt_I120(0.05, 0.05)
+ self.calib.opt_I120(search_radius, search_radius)
  self.progress_update.emit((85, 'Writing Metadata...'))
 
  self._check_abort()
 
  def _calibrate_5state(self):
 
+ search_radius = np.min((self.calib.swing, 0.05))
+
  self.calib.calib_scheme = '5-State'
 
  # Optimize Extinction State
@@ -268,19 +272,19 @@ def _calibrate_5state(self):
  self._check_abort()
 
  # Optimize 45 deg state
- self.calib.opt_I45(0.05, 0.05)
+ self.calib.opt_I45(search_radius, search_radius)
  self.progress_update.emit((65, 'Calibrating State 3...'))
 
  self._check_abort()
 
  # Optimize 90 deg state
- self.calib.opt_I90(0.05, 0.05)
+ self.calib.opt_I90(search_radius, search_radius)
  self.progress_update.emit((75, 'Calibrating State 4...'))
 
  self._check_abort()
 
  # Optimize 135 deg state
- self.calib.opt_I135(0.05, 0.05)
+ self.calib.opt_I135(search_radius, search_radius)
  self.progress_update.emit((85, 'Writing Metadata...'))
 
  self._check_abort()

recOrder/scripts/repeat_calibration.py

@@ -0,0 +1,28 @@
+# This script can be modified to debug and test calibrations
+
+import napari
+import time
+import matplotlib.pyplot as plt
+from recOrder.plugin.widget.main_widget import MainWidget
+
+save_dir = "./"
+swings = [0.1, 0.03, 0.01, 0.005]
+repeats = 5
+
+def main():
+ viewer = napari.Viewer()
+ recorder = MainWidget(viewer)
+ viewer.window.add_dock_widget(recorder)
+ recorder.ui.qbutton_gui_mode.click()
+ recorder.calib_scheme = '5-State'
+
+ for repeat in range(repeats):
+ for swing in swings:
+ print("Calibrating with swing = " + str(swing))
+ recorder.swing = swing
+ recorder.directory = save_dir 
+ recorder.run_calibration()
+ time.sleep(100)
+
+if __name__ == "__main__":
+ main()