def StackExt(self, start, stop, step=0.2, verbose=True):
init_loc = self.zst.getPosition()
no = int((stop - start) / step) + 1
pos = start
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
self.data = N.zeros((no, xs, ys), N.uint16)
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
time.sleep(0.2) # was 0.05
for p in range(no):
self.zst.setPositionf(pos)
daq.CCDTrig_run(self.handleA, self.handleB)
q = self.ccd.WaitForNewData()
print(p, q)
self.data[p] = self.ccd.images
pos += step
time.sleep(self.delay)
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.prior.getPosition()
xx = cur_pos[0]
yy = cur_pos[1]
self.stackTags(xx,
yy,
start,
stop,
step,
function='Z-Stack Widefield',
ps=89)
self.zst.setPositionf(init_loc)
return True
def singleSnapExt(self, verbose=True):
pos = self.zst.getPosition()
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
self.data = N.zeros((xs, ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
self.ccd.Acquire()
time.sleep(0.2) # was 0.05
daq.CCDTrig_run(self.handleA, self.handleB)
self.ccd.WaitForNewData()
self.data[:, :] = self.ccd.images
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.prior.getPosition()
xx = cur_pos[0]
yy = cur_pos[1]
self.stackTags(xx,
yy,
z1=pos,
z2=pos,
zs=0.,
function='Single snap',
ps=89)
return True
def TimeLapseExt(self, no=200, pol=0, verbose=True):
pos = self.zst.getPosition()
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
self.data = N.zeros((no, xs, ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
time.sleep(0.01)
self.zst.setPositionf(pos)
self.pol.MoveAbs(pol)
for p in range(no):
self.zst.setPositionf(pos)
time.sleep(0.01)
daq.CCDTrig_run(self.handleA, self.handleB)
q = self.ccd.WaitForNewData()
print(p, q)
self.data[p] = self.ccd.images
time.sleep(0.01)
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.prior.getPosition()
xx = cur_pos[0]
yy = cur_pos[1]
self.stackTags(xx,
yy,
pos,
pos,
zs=0.,
function='Time-Lapse widefield',
ps=89)
return True
def SHWFSExt(self):
self.cam.record(number_of_images=self.number_of_images,
mode='ring buffer')
daq.CCDTrig_run(self.handleA, self.handleB)
ca = self.cam.rec.get_status()
img, meta = self.cam.image(-1)
self.cam.stop()
return img
def Stack_Patterns(self, start, stop, step=0.2, verbose=True):
init_loc = self.zst.getPosition()
rots = self.pol_array
no = int((stop - start) / step) + 1
pos = start
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
psz = 15
phs = int(psz / 3)
self.data = N.zeros((psz * no, xs, ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
time.sleep(0.05) # was 0.2, changed 20141114
for p in range(no):
self.zst.setPositionf(pos)
for w in range(3):
self.pol.MoveAbs(rots[w])
time.sleep(0.4)
for m in range(phs):
qx.selecteorder(15 * self.l + phs * w + m)
qx.activate()
time.sleep(0.02)
daq.CCDTrig_run(self.handleA, self.handleB)
q = self.ccd.WaitForNewData()
print(p, q)
self.data[psz * p + 5 * w + m] = self.ccd.images
qx.deactivate()
time.sleep(0.02)
pos += step
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.prior.getPosition()
self.zst.setPositionf(init_loc)
xx = cur_pos[0]
yy = cur_pos[1]
self.stackTags(xx,
yy,
start,
stop,
step,
function='Z-Stack 3DSIM patterns',
ps=89)
return True
def Stack_Sectioning(self, start, stop, step=0.2, verbose=True):
init_loc = self.zst.getPosition()
no = int((stop - start) / step) + 1
pos = start
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
psz = 3
self.data = N.zeros((psz * no, xs, ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
self.pol.MoveAbs(0)
time.sleep(0.3)
for p in range(no):
self.zst.setPositionf(pos)
for m in range(psz):
qx.selecteorder(30 + m)
qx.activate()
time.sleep(0.02)
daq.CCDTrig_run(self.handleA, self.handleB)
q = self.ccd.WaitForNewData()
print(p, q)
self.data[psz * p + m] = self.ccd.images
qx.deactivate()
time.sleep(0.02)
pos += step
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.prior.getPosition()
self.zst.setPositionf(init_loc)
xx = cur_pos[0]
yy = cur_pos[1]
self.stackTags(xx,
yy,
start,
stop,
step,
function='Z-Stack OS patterns',
ps=89)
return True
def Image_Patterns(self, angle=0, no=200, pol=0, verbose=True):
pos = self.zst.getPosition()
xs = self.ccd.image_size[0]
ys = self.ccd.image_size[1]
psz = 5
self.data = N.zeros((psz * no, xs, ys), dtype=N.uint16)
self.ccd.SetShutterMode(1)
q = self.ccd.Acquire()
time.sleep(0.01) # was 0.2, changed 20141114
self.zst.setPositionf(pos)
for p in range(no):
for m in range(angle * 5, psz + angle * 5):
self.pol.MoveAbs(pol)
qx.selecteorder(15 * self.l + m)
qx.activate()
daq.CCDTrig_run(self.handleA, self.handleB)
q = self.ccd.WaitForNewData()
print(p, q)
self.data[psz * p + m % 5] = self.ccd.images
qx.deactivate()
time.sleep(self.delay)
self.ccd.AbortAcquisition()
self.ccd.SetShutterMode(2)
if verbose:
T.imshow(self.data, vmin=self.data.min(), vmax=self.data.max())
cur_pos = self.prior.getPosition()
xx = cur_pos[0]
yy = cur_pos[1]
self.stackTags(xx,
yy,
z1=pos,
z2=pos,
zs=0.,
function='Signle plane SIM patterns',
ps=89)
return True
def dont_get_img(self):
daq.CCDTrig_run(self.handleA, self.handleB)
def get_img(self):
daq.CCDTrig_run(self.handleA, self.handleB)
self.ccd.WaitForNewData()
self.data[:, :] = self.ccd.images