def initializeJeol(self):
# 1. checking the communication to microscope
if ToTEM.GetCheckMicroscope() != 0:
print 'Communication Error: Jeol 3100 is not ready to serve.'
return
# 2.1 setting the mag mode LowMag and defining low mag focus for the future defocus
ToTEM.SelectFunctionMode(self.LowMAG)
ToTEM.SetOM(self.theObjectMini)
self.theFocusLowMAG = self.theObjectMini
# 2.2 setting the mag mode LMAG and defining focus for the future defocus
ToTEM.SelectFunctionMode(self.MAG1)
# 3. defining focus plane for the future defocus length
ToTEM.SetOLFine(self.theObjectLensFine)
ToTEM.SetOLCoarse(self.theObjectLensCoarse)
self.theFocusMAG1 = self.theObjectLensFine + (
self.theObjectLensCoarse * 32)
print 'Jeol is MAG1 mode and focus is defined for the future defocus.'
# 4. initializing screen position as 'up'
ToTEM.SetScreen(1)
self.theScreenPos = 'up'
# 5. MDS photo mode is set for film recording
if ToTEM.GetMDSMode() != 3:
ToTEM.SetMDSMode(3)
return
def setDefocus(self, defocus, relative="absolute"):
if defocus == 0.0:
if self.theMagMode == self.LowMAG:
ToTEM.SetOM(self.theFocusLowMAG)
elif self.theMagMode == self.MAG1:
focus = self.theFocusMAG1
focus_coarse = int(focus / 32)
focus_fine = focus - (focus_coarse * 32)
print 'focus coarse:', focus_coarse, 'fine:', focus_fine
ToTEM.SetOLCoarse(focus_coarse)
ToTEM.SetOLFine(focus_fine)
else:
pass
return 0
if relative == 'relative':
defocus += self.getDefocus()
elif relative == 'absolute':
pass
print self.theMagMode
if self.theMagMode == self.LowMAG:
defocus_steps = int(round(defocus / 0.00000001))
ToTEM.SetOM(self.theFocusLowMAG + defocus_steps)
elif self.theMagMode == self.MAG1:
defocus_steps = int(round(defocus / 0.0000000058))
focus = self.theFocusMAG1 + defocus_steps
focus_coarse = int(focus / 32)
focus_fine = focus - (focus_coarse * 32)
print 'focus coarse:', focus_coarse, 'fine:', focus_fine
ToTEM.SetOLCoarse(focus_coarse)
ToTEM.SetOLFine(focus_fine)
else:
return 1
return 0