def setBeamBlank(self, bb):
if bb == "off":
ToTEM.SetBeamBlank(0)
elif bb == "on":
ToTEM.SetBeamBlank(1)
else:
raise ValueError
def setImageShift(self, vector, relative = "absolute"): shift = self.getImageShift() if relative == "relative": try: vector["x"] += shift["x"] vector["y"] += shift["y"] except KeyError: pass elif relative == "absolute": pass else: raise ValueError try: shift['x'] = vector['x'] except KeyError: pass try: shift['y'] = vector['y'] except KeyError: pass if self.theMagMode == self.LowMAG: x_shift = int(round(shift['x'] / self.IMAGESHIFT_FACTOR_X_LowMAG)) y_shift = int(round(shift['y'] / self.IMAGESHIFT_FACTOR_Y_LowMAG)) ToTEM.SetImageShift2(x_shift + self.IMAGESHIFT_ORIGIN_X, y_shift + self.IMAGESHIFT_ORIGIN_Y) else: x_shift = int(round(shift['x'] / self.IMAGESHIFT_FACTOR_X)) y_shift = int(round(shift['y'] / self.IMAGESHIFT_FACTOR_Y)) ToTEM.SetImageShift1(x_shift + self.IMAGESHIFT_ORIGIN_X, y_shift + self.IMAGESHIFT_ORIGIN_Y) print "set image shift (leginon): ", shift['x'], shift['y'] print "set image shift (jeol): ", x_shift, y_shift
def setLowDose(self, ld):
if ld == "off":
ToTEM.EndMDSMode()
elif ld == "on":
ToTEM.SetMDSMode(1)
else:
raise ValueError
def getBeamBlank(self):
if ToTEM.GetBeamBlank() == 0:
return "off"
elif ToTEM.GetBeamBlank() == 1:
return "on"
else:
raise SystemError
def getLowDoseMode(self):
if ToTEM.GetMDSMode() == 3:
return "exposure"
elif ToTEM.GetMDSMode() == 2:
return "focus1"
elif ToTEM.GetMDSMode() == 1:
return "search"
else:
return "unknown"
def setDiffractionMode(self, mode):
if mode == "imaging":
ToTEM.SelectFunctionMode(0)
elif mode == "diffraction":
ToTEM.SelectFunctionMode(4)
else:
raise ValueError
return 0
def setMainScreenPosition(self, pos):
self.theScreenPos = pos
if (pos == 'up'):
ToTEM.SetScreen(1)
elif (pos == 'down'):
ToTEM.SetScreen(0)
else:
raise KeyError
return 0
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 preFilmExposure(self, value):
if not value:
return
if ToTEM.GetUnused() < 1:
raise RuntimeError('No film to take exposure')
ToTEM.LoadFilm()
time.sleep(6)
return
def setLowDoseMode(self, mode):
if mode == "exposure":
ToTEM.SetMDSMode(3)
elif mode == "focus1":
ToTEM.SetMDSMode(2)
elif mode == "focus2":
ToTEM.SetMDSMode(2)
elif mode == "search":
ToTEM.SetMDSMode(1)
else:
raise ValueError
def getDefocus(self):
if self.theMagMode == self.LowMAG:
focus_mini = ToTEM.GetOM()
defocus_steps = focus_mini - self.theFocusLowMAG
return defocus_steps * 0.00000001
elif self.theMagMode == self.MAG1:
focus_fine = ToTEM.GetOLFine()
focus_coarse = ToTEM.GetOLCoarse()
focus = focus_fine + (focus_coarse * 32)
defocus_steps = focus - self.theFocusMAG1
return defocus_steps * 0.0000000058
else:
return 0.0
def resetDefocus(self, value):
if not value:
return 1
if self.theMagMode == self.LowMAG:
self.theFocusLowMAG = ToTEM.GetOM()
elif self.theMagMode == self.MAG1:
focus_fine = ToTEM.GetOLFine()
focus_coarse = ToTEM.GetOLCoarse()
self.theFocusMAG1 = focus_fine + (focus_coarse * 32)
return 0
else:
return 1
def postFilmExposure(self, value):
if not value:
return
ToTEM.EjectFilm()
return
def setMagnificationIndex(index):
key = self.theScreenPos
for mag in self.magTable:
if mag['index'] == index + 1:
self.theMagMode = ToTEM.SetMagnification(mag['down'])
return 0
return 1
def setMagnification(self, mag_value):
key = self.theScreenPos
for mag in self.magTable:
if mag[key] == mag_value:
self.theMagMode = ToTEM.SetMagnification(mag['down'])
return 0
return 1
def getImageShift(self):
if self.theMagMode == self.LowMAG:
shift = ToTEM.GetImageShift2()
shift_x = shift[0] - self.IMAGESHIFT_ORIGIN_X
shift_y = shift[1] - self.IMAGESHIFT_ORIGIN_Y
#print "get image shift (jeol): ", shift_x, shift_y;
return {"x" : self.IMAGESHIFT_FACTOR_X_LowMAG * shift_x, "y" : self.IMAGESHIFT_FACTOR_Y_LowMAG * shift_y}
else:
shift = ToTEM.GetImageShift1()
shift_x = shift[0] - self.IMAGESHIFT_ORIGIN_X
shift_y = shift[1] - self.IMAGESHIFT_ORIGIN_Y
#print "get image shift (jeol): ", shift_x, shift_y;
return {"x" : self.IMAGESHIFT_FACTOR_X * shift_x, "y" : self.IMAGESHIFT_FACTOR_Y * shift_y}
def getStagePosition(self):
stagePosition = ToTEM.GetStagePosition()
position = {"x" : stagePosition[0]/1000000000,
"y" : stagePosition[1]/1000000000,
"z" : stagePosition[2]/1000000000,
"a" : stagePosition[3],
"b" : stagePosition[4]}
return position
def getBeamTilt(self):
tilt = ToTEM.GetBeamTilt()
tilt_x = (tilt[0] - self.BEAMTILT_ORIGIN_X)
tilt_y = (tilt[1] - self.BEAMTILT_ORIGIN_Y)
return {
"x": tilt_x * self.BEAMTILT_FACTOR_X,
"y": tilt_y * self.BEAMTILT_FACTOR_Y
}
def getBeamShift(self):
shift = ToTEM.GetBeamShift()
shift_x = shift[0] - self.BEAMSHIFT_ORIGIN_X
shift_y = shift[1] - self.BEAMSHIFT_ORIGIN_Y
if self.theMagMode == self.LowMAG:
return {"x" : shift_x * self.BEAMSHIFT_FACTOR_X_LowMAG, "y" : shift_y * self.BEAMSHIFT_FACTOR_Y_LowMAG}
elif self.theMagMode == self.MAG1:
return {"x" : shift_x * self.BEAMSHIFT_FACTOR_X, "y" : shift_y * self.BEAMSHIFT_FACTOR_Y}
def setSpotSize(self, ss, relative="absolute"):
if relative == "relative":
ss += self.getSpotSize()
elif relative == "absolute":
pass
else:
raise ValueError
ToTEM.SetSpotSize(ss)
def setIntensity(self, intensity, relative="absolute"):
if relative == "relative":
intensity += self.getIntensity()
elif relative == "absolute":
pass
else:
raise ValueError
ToTEM.SetBrightness(int(round(intensity * self.MAX)))
return 0
def getDiffractionMode(self):
mode = ToTEM.GetFunctionMode()
if mode == 0:
return "imaging"
elif mode == 1:
return "imaging"
elif mode == 4:
return "diffraction"
else:
raise SystemError
def getMagnification(self):
key = self.theScreenPos
mag_value = ToTEM.GetMagnification()
print mag_value
for mag in self.magTable:
if mag['down'] == mag_value:
return mag[key]
def setStigmator(self, stigs, relative="absolute"):
for key in stigs.keys():
stigmators = self.getStigmator()
if key == "condenser":
stigmator = stigmators["condenser"]
elif key == "objective":
stigmator = stigmators["objective"]
elif key == "diffraction":
stigmator = stigmators["diffraction"]
else:
raise ValueError
if relative == "relative":
try:
stigs[key]["x"] += stigmator["x"]
stigs[key]["y"] += stigmator["y"]
except KeyError:
pass
elif relative == "absolute":
pass
else:
raise ValueError
try:
stigmator["x"] = stigs[key]["x"]
stigmator["y"] = stigs[key]["y"]
except KeyError:
pass
if key == "condenser":
ToTEM.SetCondenserStigmator(self.toJeol(stigmator["x"]),
self.toJeol(stigmator["y"]))
elif key == "objective":
ToTEM.SetObjectiveStigmator(self.toJeol(stigmator["x"]),
self.toJeol(stigmator["y"]))
elif key == "diffraction":
ToTEM.SetIntermediateStigmator(self.toJeol(stigmator["x"]),
self.toJeol(stigmator["y"]))
else:
raise ValueError
def getStigmator(self):
stigs = ToTEM.GetStigmator()
return {
"condenser": {
"x": self.toLeginon(stigs[0]),
"y": self.toLeginon(stigs[1])
},
"objective": {
"x": self.toLeginon(stigs[2]),
"y": self.toLeginon(stigs[3])
},
"diffraction": {
"x": self.toLeginon(stigs[4]),
"y": self.toLeginon(stigs[5])
}
}
def setGunShift(self, vector, relative = "absolute"): currentShift = self.getGunShift() if relative == "relative": try: vector["x"] += currentShift[0] vector["y"] += currentShift[1] except KeyError: pass elif relative == "absolute": pass else: raise ValueError try: ToTEM.SetGunShift(self.toJeol(vector["x"]), self.toJeol(vector["y"])) except KeyError: pass return 0
def setBeamTilt(self, vector, relative = "absolute"):
if relative == "relative":
tilt = self.getBeamTilt()
try:
vector["x"] += tilt["x"]
vector["y"] += tilt["y"]
except KeyError:
pass
elif relative == "absolute":
pass
else:
raise ValueError
tilt_x = int(round(vector['x'] / self.BEAMTILT_FACTOR_X)) + self.BEAMTILT_ORIGIN_X
tilt_y = int(round(vector['y'] / self.BEAMTILT_FACTOR_Y)) + self.BEAMTILT_ORIGIN_Y
print ">>>>>>>>>>>>>>>>> Set Beam Tilt : (", tilt_x, tilt_y, ")"
try:
ToTEM.SetBeamTilt(tilt_x, tilt_y)
except KeyError:
pass
def setBeamShift(self, vector, relative="absolute"):
shift = self.getBeamShift()
if relative == "relative":
try:
vector["x"] += shift["x"]
vector["y"] += shift["y"]
except KeyError:
pass
elif relative == "absolute":
pass
else:
raise ValueError
try:
shift['x'] = vector['x']
except KeyError:
pass
try:
shift['y'] = vector['y']
except KeyError:
pass
if self.theMagMode == self.LowMAG:
x_shift = int(round(shift["x"] / self.BEAMSHIFT_FACTOR_X_LowMAG))
y_shift = int(round(shift["y"] / self.BEAMSHIFT_FACTOR_Y_LowMAG))
elif self.theMagMode == self.MAG1:
x_shift = int(round(shift["x"] / self.BEAMSHIFT_FACTOR_X))
y_shift = int(round(shift["y"] / self.BEAMSHIFT_FACTOR_Y))
print "beam shift", x_shift, y_shift
try:
ToTEM.SetBeamShift(x_shift + self.BEAMSHIFT_ORIGIN_X,
y_shift + self.BEAMSHIFT_ORIGIN_Y)
except KeyError:
pass
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
def getLowDose(self):
ld = ToTEM.GetMDSMode()
if (ld == 0):
return "off"
else:
return "on"