Hello,
I’ve successfully built confocal microscope. Here is the picture of 1 euro star from this microscope:
Now I’m trying to optimize my program to make it work with smaller steps (link to old documentation):
def micronToStep(v):
#approximately 62nm/step
return round((v * 1000)/62)
def mz(self, position, absolute=True):
"""Move the stage to a given position.
WARNING! If you specify zeros, the stage might move a long way, as
the default is absolute moves. Position should be a dictionary
with keys called "x", "y", and "z", although we will (for now) also
accept an iterable of three numbers.
"""
try:
pos = {k: int(position[k]) for k in ["x", "y", "z", "z2"]}
except:
pos = {k: int(position[i]) for i, k in enumerate(["x", "y", "z", "z2"][:len(position)])}
pos['absolute'] = absolute
response = self.post_json("/extensions/com.openflexure.stage-mapping/actions/stage/move-measure/MeasureZAPI", pos)
return response
#microscope = ofm_client.find_first_microscope()
microscope = ofm_client.MicroscopeClient("192.168.0.100")
microscope.measureZ = mz
# homing routine
pos = microscope.position
print("Current position: " + json.dumps(pos))
print("Homing")
pos['x'] = 0
pos['y'] = 0
pos['z'] = 0
#microscope.move(pos)
#zStep = 20
#maxValue = -1
#maxPosition = -1
#for z in range(micronToStep(-2000), micronToStep(2000), micronToStep(zStep)):
# pos = microscope.position
# pos['x'] = 0
# pos['y'] = 0
# pos['z'] = z
# values = microscope.moveMeasure(microscope, pos, 1)
# #values = [a for a in values if a >= 0 ]
# values = np.asarray(values)
# value = np.median(values)
# if (value > maxValue):
# maxValue = value
# maxPosition = z
# print(value, maxValue, maxPosition)
#print("Final values:", maxValue, maxPosition)
# units in microns
xyStep = 5
xRange = 800
yRange = 800
zRange = 400
#zBase = maxPosition - micronToStep(zRange/2)
#zBase = -((30000 - 15000)/2)
zBase = 0
saveData = {
"xyStep": xyStep,
"xRange": xRange,
"yRange": yRange,
"zRange": zRange,
"zBase": zBase,
"data": [[0] * ceil(xRange/xyStep) for i in range(ceil(yRange/xyStep))],
}
measurements = 1
pos = microscope.position
print("Current position: " + json.dumps(pos))
starting_pos = microscope.position
#figure(figsize=(20,5))
ix = 0
iy = 0
totalElapsed = 0
stepsTaken = 1
maxSteps = (xRange/xyStep) * (yRange/xyStep)
up = True
ix = 0
for x in range(-micronToStep(xRange/2), micronToStep(xRange/2) - micronToStep(xyStep), micronToStep(xyStep)):
iy = 0
for y in range(-micronToStep(yRange/2), micronToStep(yRange/2) - micronToStep(xyStep), micronToStep(xyStep)):
start = timer()
values = []
if (up):
pos = {}
pos['x'] = x
pos['y'] = y
pos['z'] = zBase - micronToStep(zRange/2)
pos['z2'] = zBase + micronToStep(zRange/2)
print("Scanning up to position:", pos)
values = microscope.measureZ(microscope, pos)
values = np.asarray(values)
thisTime = timer() - start
totalElapsed += thisTime
up = False
else:
pos = {}
pos['x'] = x
pos['y'] = y
pos['z'] = zBase + micronToStep(zRange/2)
pos['z2'] = zBase - micronToStep(zRange/2)
print("Scanning to position:", pos)
values = microscope.measureZ(microscope, pos)
values = np.asarray(values)
values = np.flip(values)
thisTime = timer() - start
totalElapsed += thisTime
up = True
#xs = np.linspace(zBase - micronToStep(zRange/2), zBase + micronToStep(zRange/2), values.shape[0])
#coef = np.polyfit(xs, values, 1)
#poly1d_fn = np.poly1d(coef)
#plt.plot(xs, values, '-ok')
#plt.axhline(y=np.median(values), color='r', linestyle='-')
#plt.xlim(0, values.shape[0])
#annot_max(xs,values)
#plt.show()
print(pos)
saveData['data'][ix][iy] = values
iy += 1
timeLeft = (maxSteps - stepsTaken) * (totalElapsed / stepsTaken) / 60 / 60
print(">>>>>>>>>>>> Estimated time left: [" + str(timeLeft) + "hr], Per Scan: [" + str(totalElapsed / stepsTaken) + "s][" + str(thisTime) + "], Total Elapsed: [" + str(totalElapsed) + "s], Scans taken: [" + str(stepsTaken) + "] out of: [" + str(maxSteps) + "]")
stepsTaken += 1
pickle.dump(saveData, open('saveData.bin', 'wb'))
ix += 1
pickle.dump(saveData, open('saveData.bin', 'wb'))
#pickle.dump(dataMaxPositions, open('dataMaxPositions.bin', 'wb'))
print("Homing")
pos['x'] = 0
pos['y'] = 0
pos['z'] = 0
microscope.move(pos)
The code above works with xyStep > 4 (micron). For smaller steps i. e. xyStep = 0.5 the condition for x in range(-micronToStep(xRange/2), micronToStep(xRange/2) - micronToStep(xyStep), micronToStep(xyStep)) is not fulfilled.
The question is what and how should I change in the code above to make it work with smaller steps e. x. xyStep = 0.6? I suppose it is connected with "data": [[0] * ceil(xRange/xyStep) for i in range(ceil(yRange/xyStep))]? I also read that the stage move in xy plane with accuracy 70 nanometers and in z height with accuracy 50 nanometers, so with that information should I modify my micronToStep() function?
Thank you very much for your help.