Merge pull request #227 from mehta-lab/rm-microscope-params

Remove microscope parameters from calibration metadata

recOrder/calib/Calibration.py

@@ -776,7 +776,7 @@ def calc_inst_matrix(self):
 
  return inst_mat
 
- def write_metadata(self, notes=None, microscope_params=None):
+ def write_metadata(self, notes=None):
 
  inst_mat = self.calc_inst_matrix()
  inst_mat = np.around(inst_mat, decimals=5).tolist()
@@ -794,8 +794,7 @@ def write_metadata(self, notes=None, microscope_params=None):
  'Black level': np.round(self.I_Black, 2),
  'Extinction ratio': self.extinction_ratio,
  'ROI (x, y, width, height)': self.ROI},
- 'Notes': notes,
- 'Microscope parameters': microscope_params
+ 'Notes': notes
  }
 
  if self.calib_scheme == '4-State':

recOrder/io/metadata_reader.py

@@ -46,7 +46,6 @@ def __init__(self, path: str):
  self.LCB_voltage = self.get_lc_voltage('LCB')
  self.Swing_measured = self.get_swing_measured()
  self.Notes = self.get_notes()
- self.Microscope_parameters = self.get_microscope_parameters()
 
  def get_summary_calibration_attr(self, attr):
  try:
@@ -162,16 +161,6 @@ def get_channel_names(self):
  val = self.json_metadata['Summary']['ChNames']
  return val
 
- def get_microscope_parameters(self):
- try:
- val = self.json_metadata['Microscope parameters']
- except KeyError:
- try:
- val = self.json_metadata['Microscope parameters']
- except KeyError:
- val = None
- return val
-
  def get_notes(self):
  try:
  val = self.json_metadata['Notes']

recOrder/plugin/widget/main_widget.py

@@ -2140,6 +2140,27 @@ def calc_extinction(self):
  extinction = self.calib.calculate_extinction(self.swing, self.calib.I_Black, extinction, state1)
  self.ui.le_extinction.setText(str(extinction))
 
+ @property
+ def _microscope_params(self):
+ """
+ A dictionary containing microscope parameters from the current GUI
+ Unused in 0.2.0 --- candidate for deletion
+ """
+ def _param_value(param_name: str, ui=self.ui):
+ # refer to main widget class ui attribute names
+ ui_attr_name = "le_" + param_name
+ param_text = ui.__getattribute__(ui_attr_name).text()
+ # handle blank string
+ return float(param_text) if param_text != '' else None
+
+ return {
+ 'n_objective_media': _param_value("n_media"),
+ 'objective_NA': _param_value("obj_na"),
+ 'condenser_NA': _param_value("cond_na"),
+ 'magnification': _param_value("mag"),
+ 'pixel_size': _param_value("ps")
+ }
+
  @Slot(bool)
  def load_calibration(self):
  """
@@ -2169,15 +2190,6 @@ def load_calibration(self):
 
  self.last_calib_meta_file = metadata_path
 
- # Update the Microscope Parameters with those from the previous calibration (if they're present)
- params = metadata.Microscope_parameters
- if params is not None:
- self.ui.le_n_media.setText(str(params['n_objective_media']) if params['n_objective_media'] is not None else '')
- self.ui.le_obj_na.setText(str(params['objective_NA']) if params['objective_NA'] is not None else '')
- self.ui.le_cond_na.setText(str(params['condenser_NA']) if params['condenser_NA'] is not None else '')
- self.ui.le_mag.setText(str(params['magnification']) if params['magnification'] is not None else '')
- self.ui.le_ps.setText(str(params['pixel_size']) if params['pixel_size'] is not None else '')
-
  # Move the load calibration function to a separate thread
  self.worker = load_calibration(self.calib, metadata)
 

recOrder/plugin/workers/calibration_workers.py

@@ -92,27 +92,9 @@ def _check_abort(self):
  self.aborted.emit()
  raise TimeoutError('Stop Requested.')
 
- @property
- def _microscope_params(self):
- """A dictionary containing microscope parameters from the current GUI"""
- def _param_value(param_name: str, ui=self.calib_window.ui):
- # refer to main widget class ui attribute names
- ui_attr_name = "le_" + param_name
- param_text = ui.__getattribute__(ui_attr_name).text()
- # handle blank string
- return float(param_text) if param_text != '' else None
-
- return {
- 'n_objective_media': _param_value("n_media"),
- 'objective_NA': _param_value("obj_na"),
- 'condenser_NA': _param_value("cond_na"),
- 'magnification': _param_value("mag"),
- 'pixel_size': _param_value("ps")
- }
-
  def _write_meta_file(self, meta_file: str):
  self.calib.meta_file = meta_file
- self.calib.write_metadata(notes=self.calib_window.ui.le_notes_field.text(), microscope_params=self._microscope_params)
+ self.calib.write_metadata(notes=self.calib_window.ui.le_notes_field.text())
 
 
 class CalibrationWorker(CalibrationWorkerBase, signals=CalibrationSignals):
@@ -383,8 +365,6 @@ def work(self):
  else:
  current_json['Notes'] = old_note + ', ' + note
 
- current_json['Microscope Parameters'] = self._microscope_params
-
  with open(self.calib_window.last_calib_meta_file, 'w') as file:
  json.dump(current_json, file, indent=1)