record chip type, motion mode and laser delay in the JFJ header

- header_appendix: chip_type, motion_mode, motion_param, fel_per_ms,
  delay_pulses, laser_delay_ns and total_delay_ns, taken from the job
  that actually runs (Jungfrau.config), not from the GUI
- laser delay read from SLAAR03-LTIM-PDLY:DELAYNS_SLOW (ns, negative:
  laser before the X-rays); total = laser - delay_pulses * fel_per;
  trigger_delay now holds the total delay
- motion_delay_pulses(): trigger to X-ray pulses per mode, same rules as
  the CTA sequences (mode 6/7 nominal)
- remove the unused manual laser_delay from the run parameters
- fix laser_pulse_energy, which was written with the trigger delay

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

app_config.py

@@ -177,7 +177,6 @@ class AppCfg(QSettings):
         'padding':10, 
         'cell_name' : 'na',
         'triggered': False, 
-        'laser_delay': '',
         'laser_pulse_energy': '',
         'num_of_on_to_1_off': '1',
         'block_size':1000,
@@ -239,6 +238,12 @@ class AppCfg(QSettings):
       _log.warning(f'post sample tube: absolute out positions created from the out deltas: {pst}')
       self.setValue(AppCfg.DFT_POS_PST, pst)
 
+    # laser_delay was a manual entry (never used): the delay is now read from the laser delay PV
+    run=self.value(AppCfg.DAQ_RUN)
+    if run and 'laser_delay' in run:
+      del run['laser_delay']
+      self.setValue(AppCfg.DAQ_RUN, run)
+
     #if AppCfg.ACTIVATE_PULSE_PICKER not in keys:
     #  self.setValue(AppCfg.ACTIVATE_PULSE_PICKER, False)
     #if AppCfg.SKIP_ESCAPE_TRANSITIONS_IF_SAFE not in keys:
@@ -522,7 +527,6 @@ verbose bits:
           {'name':'prefix',             'value':daq_run['prefix'],             'type':'str'},
           {'name':'padding',            'value':daq_run['padding'],            'type':'int'}, #at some point move to old_daq_config
           {'name':'cell_name',          'value':daq_run['cell_name'],          'type':'str'}, #at some point move to old_daq_config
-          {'name':'laser_delay',        'value':daq_run['laser_delay'],        'type':'str'},
           {'name':'laser_pulse_energy', 'value':daq_run['laser_pulse_energy'], 'type':'str'}, 
           {'name':'triggered',          'value':daq_run['triggered'],          'type':'bool'},
           {'name':'num_of_on_to_1_off', 'value':daq_run['num_of_on_to_1_off'], 'type':'int', 'limits':(1, 6)}, 

psi_device.py

@@ -6,6 +6,44 @@ _log=logging.getLogger(__name__)
 class DataCollectionAbort(Exception):
     """Raised when acquisition configuration is invalid and the current scan should abort."""
 
+LASER_DELAY_PV='SLAAR03-LTIM-PDLY:DELAYNS_SLOW' # fine laser delay in ns, negative: laser before the X-rays
+MOTION_KEYS=('cnt', 'scale', 'dwell', 'tmove', 'twait', 'ssz', 'smv', 'sdelay', 'use_trf') # recorded motion parameters
+
+def motion_delay_pulses(mode, param):
+  '''
+  FEL pulses from the trigger (laser/droplet) to the X-ray pulse on the same aperture, as defined by the
+  CTA sequences in Jungfrau.config:
+    mode 1,3,4: 0 (same pulse)
+    mode 5:     twait//tmove
+    mode 6:     ssz[0]*ssz[1] (nominal: probe pass in the same aperture order as the pump pass)
+    mode 7:     ssz[0]*ssz[1]*(twait//tmove+1)+twait//tmove (nominal, as mode 6)
+  raises KeyError/ValueError/TypeError if a needed parameter is missing or invalid
+  '''
+  mode=int(mode)
+  if mode in (5, 7):
+    tmove=param['tmove']
+    wait=int(param['twait']//tmove) if tmove else 0
+    if mode==5:
+      return wait
+    sx, sy=param['ssz']
+    return int(sx)*int(sy)*(wait+1)+wait
+  if mode==6:
+    sx, sy=param['ssz']
+    return int(sx)*int(sy)
+  return 0
+
+def total_delay_ns(pulses, fel_per_ms, laser_delay_ns):
+  '''laser to X-ray delay in ns (negative: laser before the X-rays)'''
+  return laser_delay_ns-pulses*fel_per_ms*1e6
+
+def _plain(v):
+  'numpy values/arrays and tuples to plain python (json header)'
+  if hasattr(v, 'tolist'):
+    return v.tolist()
+  if isinstance(v, (tuple, list)):
+    return [_plain(x) for x in v]
+  return v
+
 logging.getLogger('matplotlib').setLevel(logging.INFO)
 
 if socket.gethostname()=='ganymede':
@@ -220,6 +258,16 @@ class Jungfrau:
     #print(kwargs)
     motion_mode = kwargs['mode']
     self.motion_mode = motion_mode
+    # recorded in the JFJ header (acquire): what actually runs, not what the main page shows
+    motion_param={k:_plain(kwargs[k]) for k in MOTION_KEYS if k in kwargs}
+    try:
+      delay_pulses=motion_delay_pulses(motion_mode, kwargs)
+    except (KeyError, ValueError, TypeError) as e:
+      _log.warning(f'delay pulses not defined for mode {motion_mode}: {e!r}')
+      delay_pulses=None
+    self.scan_meta={'chip_type':kwargs.get('chip_type', ''), 'motion_mode':int(motion_mode),
+                    'motion_param':motion_param, 'delay_pulses':delay_pulses}
+    _log.info(f'scan meta: {self.scan_meta}')
 
     if loc['jungfraujoch']:
       try:
@@ -563,8 +611,21 @@ class Jungfrau:
       geometry_file_location  = loc['geometry_file_location']
       trigger_event  = loc['event_trigger']
       trigger_flag   = run['triggered']
-      trigger_delay  = run['laser_delay']
       laser_energy = run['laser_pulse_energy']
+      dt_misc = cfg.value(AppCfg.DT_MISC)
+      fel_per = dt_misc['fel_per']
+      try:
+        laser_delay_ns = float(epics.caget(LASER_DELAY_PV, timeout=1.0))
+      except (TypeError, ValueError):
+        _log.warning(f'laser delay: no value from {LASER_DELAY_PV}')
+        laser_delay_ns = None
+      scan_meta = getattr(self, 'scan_meta', {})
+      delay_pulses = scan_meta.get('delay_pulses')
+      if delay_pulses is None or laser_delay_ns is None:
+        trigger_delay = None
+      else:
+        trigger_delay = total_delay_ns(delay_pulses, fel_per, laser_delay_ns)
+      _log.info(f'delay: {delay_pulses} pulses x {fel_per} ms + laser {laser_delay_ns} ns = {trigger_delay} ns')
       
       transmission_ATT53 = epics.caget("SARFE10-OATT053:UsrRec.TD")
       transmission_ATT150 = epics.caget("SAROP31-OATA150:UsrRec.TD")
@@ -590,9 +651,16 @@ class Jungfrau:
 
       header_appendix['geometry_file_location'] = geometry_file_location
       header_appendix['trigger_flag'] = trigger_flag
-      header_appendix['trigger_delay'] = trigger_delay
+      header_appendix['trigger_delay'] = trigger_delay # total delay in ns (same as total_delay_ns)
       header_appendix['trigger_event'] = trigger_event
-      header_appendix['laser_pulse_energy'] = trigger_delay
+      header_appendix['laser_pulse_energy'] = laser_energy
+      header_appendix['chip_type'] = scan_meta.get('chip_type', '')
+      header_appendix['motion_mode'] = scan_meta.get('motion_mode')
+      header_appendix['motion_param'] = scan_meta.get('motion_param', {})
+      header_appendix['fel_per_ms'] = fel_per
+      header_appendix['delay_pulses'] = delay_pulses
+      header_appendix['laser_delay_ns'] = laser_delay_ns
+      header_appendix['total_delay_ns'] = trigger_delay
       header_appendix['file_prefix'] = f'run{run_number:04}-{user_tag}'
       try:
           self.jfj.acquire(

swissmx.py

@@ -1593,6 +1593,7 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
         except AttributeError as e:
           _log.warning(f'no scan parameters for object->skipped:{go}')
           continue
+        param['chip_type']=getattr(go, '_chip_type', t.__name__) # recorded in the JFJ header
         vb=self.vb
         grp=self._goTracked
         mft=self._moduleFixTarget
@@ -2262,6 +2263,7 @@ object settings:
       go=UsrGO.Path((fx-sz[0]/2, fy-sz[1]/2), sz, gp.points, fiducial, fidScl,**param)
     else:
       _log.error('index not handeled')
+    go._chip_type=mft._cbType.currentText() # recorded in the JFJ header
 
     grp=self._goTracked
     grp.addItem(go)