ScriptName SPSetUp

ErrorsToLog 
# **** Zeroing Flags ****
SevereCrashFlag := 0
AutoFocusFailedCounter := 0
CountUpFromFocus := 0
StopRunFlag := 0
SkipFlag := 0

ReportStageXYZ 
LastFocX := $ReportedValue1
LastFocY := $ReportedValue2
LastFocZ := $ReportedValue3

# Checking if a defferd sum is wating
IsVariableDefined DeferredSumIsWatingFlg
If 	$ReportedValue1 == 0
	DeferredSumIsWatingFlg := 0
Elseif $DeferredSumIsWatingFlg == 1
	GetDeferredSum
	OpenFrameSumFile _sum.mrc
	Save
	#AddToAutodoc NavItem $PrevNavItem
	#AddToAutodoc AccelerationVoltage_kV 300
	#AddToAutodoc StageErrorXY_nm $PrevStageErrorX $PrevStageErrorY
	#AddToAutodoc NumberOfNavItemsSinceLastAutoFocus $PrevCountUpFromFocus
	#AddToAutodoc STDevOfLastAutoFocus_um $PrevSTDDefocus
	#AddToAutodoc TargetDefocus_um $prevDeFocusForMicrograph
	#AddToAutodoc EstiamtedZeroDefocus_um $PrevZeroDeFocus
	#AddToAutodoc LensesSettlingTime_sec $MeasuredLensesSettlingTime
	#AddToAutodoc StageSettlingTime_sec $TimeUpToRecored
	#AddToAutodoc TotalDataAcquisitionTime_sec $PrevTotalDataCollectionTime 
	#WriteAutodoc		
	echo *!* Info_for $FrameSumFileName
	echo *!* NavItem $PrevNavItem
	echo *!* AccelerationVoltage_kV 300
	echo *!* StageError_nm $PrevStageError 
	echo *!* NumberOfNavItemsSinceLastAutoFocus $PrevCountUpFromFocus
	#echo *!* STDevOfLastAutoFocus_um $PrevSTDDefocus
	echo *!* TargetDefocus_um $PrevTargetDefocus
	echo *!* NominalZeroDeFocus_um  $PrevNominalZeroDeFocus
	echo *!* NominalDefocus_um $PrevNominalDefocus 
	echo *!* LensesSettlingTime_sec $PervLensesSettlingTime 
	echo *!* StageSettlingTime_sec $PervStageSettlingTime 
	echo *!* TotalDataAcquisitionTime_sec $PrevTotalDataCollectionTime 
			
	CloseFile
	DeferredSumIsWatingFlg := 0

	CloseFile
	DeferredSumIsWatingFlg := 0
EndIf

# Settling Times
PreFocusSettling := 15 # [sec]
PreRecordStageSettling := 60 # [sec]
PreRecordLensSettling := 15 # [sec]

# ***  Defocus data collection range ***
DefocusList := {-2.5 -2 -1.5 -1.25 -1.25 -1}  # Traget defocus values in um
sz_DefocusList := $#DefocusList

echo Target defocus list: $DefocusList
echo The list can be changed by: editing the DefocusList decleration above or in in the script ResetSP ****

# *** AutoFocus policy ***
#ReportDefocus
CurrentZeroDeFocus := 0
NominalZeroDefocus := $CurrentZeroDeFocus 
echo $CurrentZeroDeFocus 

FocusBeforRecord := 0
AutoFocusLoopRepeat := 3
STDDefocusTH := 100 # Allowed Variance in DeFocus determination

DoAutoFocusEvery := 8         # Number of Recoreded iamges between Autofocus
DoAutoFocusZMoveTH := 0.1     # [um]  Z change between AutoFocus
DoAutoFocusLateralMoveTH := 10 # [um]  Distance between AutoFocus
AllowedConscutiveBadAF := 3   # Number of allowed consecutive falure to get reliable AutoFocus before halting run

# *** Locking on target policy
NumTargetingLoops := 2
PosErr_TH := 0.15      # Stage posstioning error for zeroing image shift 

# *** Microscope Housekipping settings ***
BufferCycleIntervalHr := 2 # {Hr]- Time between Buffer Cycles
DarkRefIntervalHr := 2 # [Hr] Time - between Dark Refrence

# Intialzaing stage postion vlaues
ReportStageXYZ   
xLastFoc := $ReportedValue1
yLastFoc := $ReportedValue2
zLastFoc := $ReportedValue3

# *** Micrograph Counter  ***
IsVariableDefined MicrographCount
If 	$ReportedValue1 == 0
	MicrographCount := 0
Else
	YesNoBox Micrograph Counter is set to: $MicrographCount Do you want to reset the Micrograph Counter?
	If 	$ReportedValue1 == 1
		MicrographCount := 0
	EndIf
EndIf


# *** Setting work-dir
#ReportDirectory CurrentDir
UserSetDirectory
WorkDir := $ReportedValue1

# ***  HouseKipping  1/2 *** 
# Taking a low-mag image in order to look at the objective apperture
TiltTo 0

ReportPercentC2
C2 = $ReportedValue1
ReportMag
Mag = $ReportedValue1
ReportSpotSize
SpotSize = $ReportedValue1

#SetBeamBlank 1
#delay 5 sec
#SetLowDoseMode 0
#SetColumnOrGunValve 1
#SetPercentC2 99
#SetSpotSize 9
#SetMag 81
#SetBeamBlank 0
#View
#SetBeamBlank 1
#SetPercentC2 $C2
#SetMag $Mag
#SetSpotSize $SpotSize
#SetLowDoseMode 1
#GoToLowDoseArea R 0

Pause Make sure that: (1) You see the objective aperture in the recently acquired low mag image. (2) The sampel is Eucentric. Sum frames and mdocs will be saved to: $WorkDir

# ***  HouseKipping part 2/2 *** 
#LongOperation BufferCycle $BufferCycleIntervalHr 
#LongOperation DarkRefrence $DarkRefIntervalHr # DDD vs Udate..
echo Ready to Run!!!