def OnInit(self):
self.HARDWARE_DEBUG = HARDWARE_DEBUG
self.frame = MCLStage3DFrame(None)
self.nanodrive = MCLNanoDrive(debug=self.HARDWARE_DEBUG)
try:
self.frame.m_staticText_maxdim.SetLabel(
"[ %g x %g x %g ]" %
(self.nanodrive.cal_X, self.nanodrive.cal_Y,
self.nanodrive.cal_Z))
except Exception as e:
print e
self.frame.m_staticText_maxdim.SetLabel("[ ? ? ? ]")
x, y, z = self.nanodrive.get_pos()
self.frame.m_scrollBar_x.SetScrollbar(100 * x / self.nanodrive.cal_X,
1,
100,
1,
refresh=True)
self.frame.m_scrollBar_y.SetScrollbar(100 * y / self.nanodrive.cal_Y,
1,
100,
1,
refresh=True)
self.frame.m_scrollBar_z.SetScrollbar(100 * z / self.nanodrive.cal_Z,
1,
100,
1,
refresh=True)
self.frame.m_textCtrl_x.SetValue("%02.3f" % x)
self.frame.m_textCtrl_y.SetValue("%02.3f" % y)
self.frame.m_textCtrl_z.SetValue("%02.3f" % z)
self.frame.m_scrollBar_x.Bind(wx.EVT_SCROLL, self.on_scroll)
self.frame.m_scrollBar_y.Bind(wx.EVT_SCROLL, self.on_scroll)
self.frame.m_scrollBar_z.Bind(wx.EVT_SCROLL, self.on_scroll)
# Figure
self.wxfig = MPLFigureWithToolbarWX(self.frame.m_panel_plot)
self.fig = self.wxfig.fig
self.ax = self.fig.add_subplot(111)
self.ax.set_xlim(0, self.nanodrive.cal_X)
self.ax.set_ylim(self.nanodrive.cal_Y, 0)
self.xypos_line, = self.ax.plot([x], [y], 'ro')
self.frame.Show()
return True
def __init__(self, **params):
for p in self.INPUT_PARAM_NAMES:
setattr(self, p, params[p])
self.x_array = np.arange(self.x0, self.x1, self.dx, dtype=float)
self.y_array = np.arange(self.y0, self.y1, self.dy, dtype=float)
self.z_array = np.arange(self.z0, self.z1, self.dz, dtype=float)
self.Nx = len(self.x_array)
self.Ny = len(self.y_array)
self.Nz = len(self.z_array)
self.mcl_axis_translation = xyz_tuple(*self.mcl_axis_translation)
self.HARDWARE_DEBUG = False
#HARDWARE
self.nanodrive = MCLNanoDrive(debug=self.HARDWARE_DEBUG)
self.mono = ActonSpectrometer(port=SPEC_COMM_PORT,
debug=self.HARDWARE_DEBUG,
dummy=False)
self.mono_grating = self.mono.read_grating()
self.mono_wl = self.mono.read_wl()
self.ccd = AndorCCD(debug=self.HARDWARE_DEBUG)
print "Andor CCD"
print "%g x %g" % (self.ccd.Nx, self.ccd.Ny)
self.spectrum_length = self.ccd.Nx
self.ccd.set_cooler_on()
self.ccd.get_temperature()
if SHOW_GRAPH:
self.fig = pl.figure(1)
self.ax = self.fig.add_subplot(111)
self.spec_plotline, = self.ax.plot(np.ones(self.spectrum_length))
self.fig.show()
#DATA ARRAYS
self.integrated_count_map = np.zeros((
self.Nz,
self.Ny,
self.Nx,
),
dtype=int)
self.spec_map = np.zeros(
(self.Nz, self.Ny, self.Nx, self.spectrum_length), dtype=np.int32)
class ConfocalSpectrum3DScan(object):
INPUT_PARAM_NAMES = """x0 x1 dx y0 y1 dy z0 z1 dz
t_exposure emgain ad_chan ad_hs_speed_index bin_row0 bin_row1
axis_scan_order mcl_axis_translation""".split()
def __init__(self, **params):
for p in self.INPUT_PARAM_NAMES:
setattr(self, p, params[p])
self.x_array = np.arange(self.x0, self.x1, self.dx, dtype=float)
self.y_array = np.arange(self.y0, self.y1, self.dy, dtype=float)
self.z_array = np.arange(self.z0, self.z1, self.dz, dtype=float)
self.Nx = len(self.x_array)
self.Ny = len(self.y_array)
self.Nz = len(self.z_array)
self.mcl_axis_translation = xyz_tuple(*self.mcl_axis_translation)
self.HARDWARE_DEBUG = False
#HARDWARE
self.nanodrive = MCLNanoDrive(debug=self.HARDWARE_DEBUG)
self.mono = ActonSpectrometer(port=SPEC_COMM_PORT,
debug=self.HARDWARE_DEBUG,
dummy=False)
self.mono_grating = self.mono.read_grating()
self.mono_wl = self.mono.read_wl()
self.ccd = AndorCCD(debug=self.HARDWARE_DEBUG)
print "Andor CCD"
print "%g x %g" % (self.ccd.Nx, self.ccd.Ny)
self.spectrum_length = self.ccd.Nx
self.ccd.set_cooler_on()
self.ccd.get_temperature()
if SHOW_GRAPH:
self.fig = pl.figure(1)
self.ax = self.fig.add_subplot(111)
self.spec_plotline, = self.ax.plot(np.ones(self.spectrum_length))
self.fig.show()
#DATA ARRAYS
self.integrated_count_map = np.zeros((
self.Nz,
self.Ny,
self.Nx,
),
dtype=int)
self.spec_map = np.zeros(
(self.Nz, self.Ny, self.Nx, self.spectrum_length), dtype=np.int32)
def run_3d_scan(self):
self.ccd.set_ro_image_mode()
self.ccd.set_trigger_mode('internal')
self.ccd.set_image_flip(ANDOR_HFLIP, ANDOR_VFLIP)
print "flip", self.ccd.get_image_flip()
self.ccd.set_ad_channel(self.ad_chan)
self.ccd.set_exposure_time(self.t_exposure)
self.ccd.set_EMCCD_gain(self.emgain)
self.ccd.set_cooler_on()
self.ccd.get_temperature()
self.ccd.set_shutter_open()
self.ccd.set_hs_speed(self.ad_hs_speed_index)
self.set_ijk = (-1, -1, -1)
self.scanning = True
time0 = time.time()
for iii, ijk in enumerate(
ijk_generator((self.Nx, self.Ny, self.Nz),
self.axis_scan_order)):
#previous ijk
ip, jp, kp = self.set_ijk
# new ijk
i, j, k = ijk
# move stage
if i != ip:
x = self.x_array[i]
self.nanodrive.set_pos_ax(x, self.mcl_axis_translation.x)
if j != jp:
y = self.y_array[j]
self.nanodrive.set_pos_ax(y, self.mcl_axis_translation.y)
if k != kp:
z = self.z_array[k]
self.nanodrive.set_pos_ax(z, self.mcl_axis_translation.z)
self.set_ijk = ijk
#t1 = time.time()
self.read_from_hardware()
#print "read_from_hardware (s)", time.time() - t1
#t1 = time.time()
self.ccd.start_acquisition()
stat = "ACQUIRING"
while stat != "IDLE":
time.sleep(self.ccd.exposure_time * 0.1)
stati, stat = self.ccd.get_status()
self.ccd.get_acquired_data()
#print "ccd acquire (s)", time.time() - t1
spectrum = np.sum(self.ccd.buffer[self.bin_row0:self.bin_row1],
axis=0)
self.spec_map[k, j, i, :] = spectrum
cts = self.integrated_count_map[k, j, i] = sum(spectrum)
if ((i + j + k) % 10) == 0:
print ijk, cts
t_now = time.time()
pixel_time = (t_now - time0) * 0.1
print "sec per pixel:", pixel_time, "| time remaining (s)", ((
(self.Nx * self.Ny * self.Nz) - iii) * pixel_time)
time0 = t_now
#if ((i + j + k) % 2) == 0 :
if True:
if SHOW_GRAPH:
self.spec_plotline.set_ydata(spectrum)
self.ax.relim()
self.ax.autoscale_view(tight=None,
scalex=False,
scaley=True)
self.fig.canvas.draw()
#Finish up after scan
print "saving data..."
save_params = self.INPUT_PARAM_NAMES + [
"spec_map", "Nx", "Ny", "Nz", "spectrum_length", "mono_grating",
"mono_wl", "x_array", "y_array", "z_array", "integrated_count_map"
]
save_dict = dict()
for key in save_params:
save_dict[key] = getattr(self, key)
t0 = time.time()
save_fname = "%i_spec_map3d.npz" % t0
np.savez_compressed(save_fname, **save_dict)
print "data saved as %s" % save_fname
def read_from_hardware(self):
pos = self.nanodrive.get_pos()
self.xpos = pos[self.mcl_axis_translation.x - 1]
self.ypos = pos[self.mcl_axis_translation.y - 1]
self.zpos = pos[self.mcl_axis_translation.z - 1]
def OnInit(self):
print "OnInit"
self.HARDWARE_DEBUG = HARDWARE_DEBUG
self.STORED_HISTCHAN = 5000
self.frame = ScanningTRPLControlFrame(None)
# Logged Quantities
self.x_position = LoggedQuantity(
name='x_position',
dtype=np.float,
display_textctrl=self.frame.m_textCtrl_current_x,
input_textctrl=self.frame.m_textCtrl_set_current_x)
self.y_position = LoggedQuantity(
name='x_position',
dtype=np.float,
display_textctrl=self.frame.m_textCtrl_current_y,
input_textctrl=self.frame.m_textCtrl_set_current_y)
# Figure
self.wxfig = MPLFigureWithToolbarWX(self.frame.m_panel_plot)
self.fig = self.wxfig.fig
self.ax = self.fig.add_subplot(111)
# Optimization Fig
self.fig2 = pl.figure(2)
self.ax2 = self.fig2.add_subplot(111)
self.c0_hist_line, = self.ax2.plot(np.zeros(HIST_LEN, dtype=float))
self.c1_hist_line, = self.ax2.plot(np.zeros(HIST_LEN, dtype=float))
self.hist_vline = self.ax2.axvline(0)
self.c0_hist = np.zeros(HIST_LEN, dtype=float)
self.c1_hist = np.zeros(HIST_LEN, dtype=float)
self.fig2.show()
self.hist_i = 0
# hardware
self.scanning = False
self.nanodrive = MCLNanoDrive(debug=self.HARDWARE_DEBUG)
try:
self.frame.m_staticText_maxdim.SetLabel(
"max: %g x %g um" %
(self.nanodrive.cal_Y, self.nanodrive.cal_X))
except Exception as e:
print e
self.frame.m_staticText_maxdim.SetLabel("max: ? x ? um")
#self.frame.m_staticText_maxdim.SetLabel("max: 75 x 75 um")
#self.srslockin = SRSlockin(port="COM5", gpibaddr=8)
#self.lockinstage = LockinStage(srs=self.srslockin,
# POSMIN=0, POSMAX=75, channels={'x':1, 'y':2, 'z':3})
self.picoharp = PicoHarp300(devnum=0, debug=self.HARDWARE_DEBUG)
self.read_from_hardware()
#self.x_position.hardware_set_func = lambda x: self.lockinstage.setx(x)
#self.y_position.hardware_set_func = lambda y: self.lockinstage.sety(y)
self.x_position.hardware_set_func = lambda x: self.nanodrive.set_pos_ax(
x, 2)
self.y_position.hardware_set_func = lambda y: self.nanodrive.set_pos_ax(
y, 1)
# update figure
self.ax.set_xlim(0, self.nanodrive.cal_Y)
self.ax.set_ylim(0, self.nanodrive.cal_X)
#self.ax.set_xlim(0, 75)
#self.ax.set_ylim(0, 75)
# events
self.frame.Bind(wx.EVT_BUTTON, self.on_start_scan,
self.frame.m_button_start)
self.frame.Bind(wx.EVT_BUTTON, self.on_stop_scan,
self.frame.m_button_stop)
self.timer = wx.Timer(id=2001)
self.timer.Bind(wx.EVT_TIMER, self.on_timer)
self.timer.Start(2000)
self.fast_timer = wx.Timer(id=2002)
self.fast_timer.Bind(wx.EVT_TIMER, self.on_fast_timer)
self.frame.m_checkBox_picoharp_fastreadout.Bind(
wx.EVT_CHECKBOX, self.on_fast_timer_checkbox)
self.update_display()
self.frame.Show()
return True
class ScanningTRPLHistMapApp(wx.App):
def OnInit(self):
print "OnInit"
self.HARDWARE_DEBUG = HARDWARE_DEBUG
self.STORED_HISTCHAN = 5000
self.frame = ScanningTRPLControlFrame(None)
# Logged Quantities
self.x_position = LoggedQuantity(
name='x_position',
dtype=np.float,
display_textctrl=self.frame.m_textCtrl_current_x,
input_textctrl=self.frame.m_textCtrl_set_current_x)
self.y_position = LoggedQuantity(
name='x_position',
dtype=np.float,
display_textctrl=self.frame.m_textCtrl_current_y,
input_textctrl=self.frame.m_textCtrl_set_current_y)
# Figure
self.wxfig = MPLFigureWithToolbarWX(self.frame.m_panel_plot)
self.fig = self.wxfig.fig
self.ax = self.fig.add_subplot(111)
# Optimization Fig
self.fig2 = pl.figure(2)
self.ax2 = self.fig2.add_subplot(111)
self.c0_hist_line, = self.ax2.plot(np.zeros(HIST_LEN, dtype=float))
self.c1_hist_line, = self.ax2.plot(np.zeros(HIST_LEN, dtype=float))
self.hist_vline = self.ax2.axvline(0)
self.c0_hist = np.zeros(HIST_LEN, dtype=float)
self.c1_hist = np.zeros(HIST_LEN, dtype=float)
self.fig2.show()
self.hist_i = 0
# hardware
self.scanning = False
self.nanodrive = MCLNanoDrive(debug=self.HARDWARE_DEBUG)
try:
self.frame.m_staticText_maxdim.SetLabel(
"max: %g x %g um" %
(self.nanodrive.cal_Y, self.nanodrive.cal_X))
except Exception as e:
print e
self.frame.m_staticText_maxdim.SetLabel("max: ? x ? um")
#self.frame.m_staticText_maxdim.SetLabel("max: 75 x 75 um")
#self.srslockin = SRSlockin(port="COM5", gpibaddr=8)
#self.lockinstage = LockinStage(srs=self.srslockin,
# POSMIN=0, POSMAX=75, channels={'x':1, 'y':2, 'z':3})
self.picoharp = PicoHarp300(devnum=0, debug=self.HARDWARE_DEBUG)
self.read_from_hardware()
#self.x_position.hardware_set_func = lambda x: self.lockinstage.setx(x)
#self.y_position.hardware_set_func = lambda y: self.lockinstage.sety(y)
self.x_position.hardware_set_func = lambda x: self.nanodrive.set_pos_ax(
x, 2)
self.y_position.hardware_set_func = lambda y: self.nanodrive.set_pos_ax(
y, 1)
# update figure
self.ax.set_xlim(0, self.nanodrive.cal_Y)
self.ax.set_ylim(0, self.nanodrive.cal_X)
#self.ax.set_xlim(0, 75)
#self.ax.set_ylim(0, 75)
# events
self.frame.Bind(wx.EVT_BUTTON, self.on_start_scan,
self.frame.m_button_start)
self.frame.Bind(wx.EVT_BUTTON, self.on_stop_scan,
self.frame.m_button_stop)
self.timer = wx.Timer(id=2001)
self.timer.Bind(wx.EVT_TIMER, self.on_timer)
self.timer.Start(2000)
self.fast_timer = wx.Timer(id=2002)
self.fast_timer.Bind(wx.EVT_TIMER, self.on_fast_timer)
self.frame.m_checkBox_picoharp_fastreadout.Bind(
wx.EVT_CHECKBOX, self.on_fast_timer_checkbox)
self.update_display()
self.frame.Show()
return True
def on_timer(self, e):
self.read_from_hardware()
self.update_display()
def on_fast_timer(self, e):
self.picoharp.read_count_rates()
self.frame.m_textCtrl_count0.SetValue(str(self.picoharp.Countrate0))
self.frame.m_textCtrl_count1.SetValue(str(self.picoharp.Countrate1))
self.c0_hist[self.hist_i] = self.picoharp.Countrate0
self.c1_hist[self.hist_i] = self.picoharp.Countrate1
#self.c0_hist_line.set_ydata(self.c0_hist)
self.c1_hist_line.set_ydata(self.c1_hist)
self.hist_vline.set_xdata([self.hist_i] * 2)
self.hist_i += 1
self.hist_i %= HIST_LEN
if (self.hist_i % 10) == 0:
self.ax2.relim()
self.ax2.autoscale_view(scalex=False, scaley=True)
#self.ax2.autoscale()
self.fig2.canvas.draw()
def on_fast_timer_checkbox(self, e):
fast_timer_enable = self.frame.m_checkBox_picoharp_fastreadout.GetValue(
)
if fast_timer_enable:
self.fast_timer.Start(100)
else:
self.fast_timer.Stop()
def on_start_scan(self, e):
print "start scan"
self.scanning = True
# get scan parameters:
self.x0 = float(self.frame.m_textCtrl_x0.GetValue())
self.x1 = float(self.frame.m_textCtrl_x1.GetValue())
self.y0 = float(self.frame.m_textCtrl_y0.GetValue())
self.y1 = float(self.frame.m_textCtrl_y1.GetValue())
self.dx = float(self.frame.m_textCtrl_dx.GetValue()) / 1000.
self.dy = float(self.frame.m_textCtrl_dy.GetValue()) / 1000.
self.x_array = np.arange(self.x0, self.x1, self.dx, dtype=float)
self.y_array = np.arange(self.y0, self.y1, self.dy, dtype=float)
self.Nx = len(self.x_array)
self.Ny = len(self.y_array)
print "Nx, Ny", self.Nx, self.Ny
self.tacq = int(float(self.frame.m_textCtrl_tacq.GetValue()) * 1000)
self.phrange = int(self.frame.m_textCtrl_phrange.GetValue())
self.phoffset = int(self.frame.m_textCtrl_phoffset.GetValue())
self.syncdiv = int(
self.frame.m_choice_syncdivider.GetString(
self.frame.m_choice_syncdivider.GetSelection()))
self.zerocross0 = int(self.frame.m_spinCtrl_zerocross0.GetValue())
self.zerocross1 = int(self.frame.m_spinCtrl_zerocross0.GetValue())
self.level0 = int(self.frame.m_textCtrl_level0.GetValue())
self.level1 = int(self.frame.m_textCtrl_level1.GetValue())
# create data arrays
#self.integrated_count_map_c0 = np.zeros((self.Nx, self.Ny), dtype=int)
self.integrated_count_map_c1 = np.zeros((self.Ny, self.Nx), dtype=int)
self.time_trace_map = np.zeros(
(self.Ny, self.Nx, self.STORED_HISTCHAN), dtype=int)
print "shape:", self.integrated_count_map_c1.shape, self.time_trace_map.shape
#update figure
self.aximg = self.ax.imshow(
self.integrated_count_map_c1,
origin='lower',
vmin=1e4,
vmax=1e5,
interpolation='nearest',
extent=[self.x0, self.x1, self.y0, self.y1])
self.wxfig.redraw()
# set up experiment
self.picoharp.setup_experiment(Range=self.phrange,
Offset=self.phoffset,
Tacq=self.tacq,
SyncDivider=self.syncdiv,
CFDZeroCross0=self.zerocross0,
CFDLevel0=self.level0,
CFDZeroCross1=self.zerocross1,
CFDLevel1=self.level1)
line_time0 = time.time()
for jj in range(self.Ny):
#self.nanodrive.SetY(self.y_array[j])
if not self.scanning:
break
y = self.y_array[jj]
#self.lockinstage.sety(y)
#self.read_from_hardware()
self.nanodrive.set_pos_ax(y, 1)
self.read_from_hardware()
y = self.ypos
print "line time:", time.time() - line_time0
print "pixel time:", float(time.time() - line_time0) / len(
self.x_array)
line_time0 = time.time()
"""xdelta = self.x_array[0] - self.xpos
if abs(xdelta) > 2.0:
if xdelta > 0:
step = +1.0
elif xdelta < 0:
step = -1.0
for x in np.arange(self.xpos, self.x_array[0], step):
self.nanodrive.set_pos_ax(x, 2)
wx_yielded_sleep(0.1)
"""
if jj % 2: #odd lines
x_line_indicies = range(self.Nx)
else: #even lines -- traverse in opposite direction
x_line_indicies = range(self.Nx)[::-1]
for ii in x_line_indicies:
if not self.scanning:
break
x = self.xpos = self.x_array[ii]
#print ii,x
wx.Yield()
#self.nanodrive.SetX(self.x_array[i])
#self.nanodrive.set_pos(x, y)
#print "nanodrive set_pos: ", x, y
#self.lockinstage.setx(x)
self.nanodrive.set_pos_ax(x, 2)
#if self.HARDWARE_DEBUG: print "lockin stage moved to ", x, y
ph = self.picoharp
ph.start_histogram(Tacq=self.tacq)
while not ph.check_done_scanning():
wx.Yield()
ph.stop_histogram()
hist_data = ph.read_histogram_data()
self.time_trace_map[jj,
ii, :] = hist_data[0:self.STORED_HISTCHAN]
self.integrated_count_map_c1[jj, ii] = sum(hist_data)
#x1, y1 = self.nanodrive.get_pos()
#print "get pos: ", x1,y1
# update display
try:
self.update_display()
except Exception, err:
print "Failed to update_display", err
if not (ii % 5):
#self.update_figure()
try:
#print "updating figure"
#self.read_from_hardware()
self.aximg.set_data(self.integrated_count_map_c1)
try:
count_min = np.min(
self.integrated_count_map_c1[np.nonzero(
self.integrated_count_map_c1)])
except Exception as err:
count_min = 0
count_max = np.max(self.integrated_count_map_c1)
self.aximg.set_clim(count_min, count_max + 1)
self.wxfig.redraw()
except Exception, err:
print "Failed to update figure:", err
def __init__(self):
ui_loader = QtUiTools.QUiLoader()
print os.path.join(__file__,"scanning_confocal_mcl_lj.ui")
ui_file = QtCore.QFile("scanning_confocal_mcl_lj.ui")
ui_file.open(QtCore.QFile.ReadOnly);
self.ui = ui_loader.load(ui_file)
ui_file.close()
self.HARDWARE_DEBUG = HARDWARE_DEBUG
self.fig2d = Figure()
self.ax2d = self.fig2d.add_subplot(111)
self.ax2d.plot([0,1])
self.canvas2d = FigureCanvas(self.fig2d)
self.ui.plot2D_verticalLayout.addWidget(self.canvas2d)
self.navtoolbar_plot2d = NavigationToolbar2(self.canvas2d, self.ui)
self.ui.plot2D_verticalLayout.addWidget( self.navtoolbar_plot2d )
self.fig_opt = Figure()
self.ax_opt = self.fig_opt.add_subplot(111)
self.canvas_opt = FigureCanvas(self.fig_opt)
self.ui.plot_optimize_verticalLayout.addWidget(self.canvas_opt)
self.navtoolbar_plot_opt = NavigationToolbar2(self.canvas_opt, self.ui)
self.ui.plot_optimize_verticalLayout.addWidget( self.navtoolbar_plot_opt )
self.optimize_history = np.zeros(OPTIMIZE_HISTORY_LEN, dtype=np.float)
self.optimize_ii = 0
self.optimize_line, = self.ax_opt.plot(self.optimize_history)
self.optimize_current_pos = self.ax_opt.axvline(self.optimize_ii, color='r')
##################### hardware #########################################
self.scanning = False
######## MCL NanoDrive Stage ###########################################
self.nanodrive = MCLNanoDrive(debug=self.HARDWARE_DEBUG)
try:
self.hmax = self.nanodrive.cal[HAXIS_ID]
self.vmax = self.nanodrive.cal[VAXIS_ID]
self.ui.maxdim_label.setText("max: %g x %g um" % (self.hmax, self.vmax) )
except Exception as e:
print e
self.ui.maxdim_label.setText("max: ? x ? um")
# Logged Quantities
self.x_position = LoggedQuantity(name = 'x_position', dtype=np.float)
self.y_position = LoggedQuantity(name = 'y_position', dtype=np.float)
self.z_position = LoggedQuantity(name = 'z_position', dtype=np.float)
#self.x_position.updated_value.connect(self.ui.cx_lcdNumber.display)
self.x_position.updated_value.connect(self.ui.cx_doubleSpinBox.setValue)
self.ui.x_set_lineEdit.returnPressed.connect(self.x_position.update_value)
#self.y_position.updated_value.connect(self.ui.cy_lcdNumber.display)
self.y_position.updated_value.connect(self.ui.cy_doubleSpinBox.setValue)
self.ui.y_set_lineEdit.returnPressed.connect(self.y_position.update_value)
#self.z_position.updated_value.connect(self.ui.cz_lcdNumber.display)
self.z_position.updated_value.connect(self.ui.cz_doubleSpinBox.setValue)
self.ui.z_set_lineEdit.returnPressed.connect(self.z_position.update_value)
self.x_position.hardware_set_func = lambda x: self.nanodrive.set_pos_ax(x, XAXIS_ID)
self.y_position.hardware_set_func = lambda y: self.nanodrive.set_pos_ax(y, YAXIS_ID)
self.z_position.hardware_set_func = lambda z: self.nanodrive.set_pos_ax(z, ZAXIS_ID)
####### LabJack (apd) counter readout ##################################
self.lj_counter = labjack_counter.LabJackCounter()
self.apd_count_rate = LoggedQuantity(name = 'apd_count_rate', dtype=np.float, fmt="%e")
self.apd_count_rate.updated_text_value.connect(self.ui.apd_counter_output_lineEdit.setText)
########################################################################
self.read_from_hardware()
self.update_display()
# update figure
self.ax2d.set_xlim(0, self.hmax)
self.ax2d.set_ylim(0, self.vmax)
# events
self.ui.scan_start_pushButton.clicked.connect(self.on_scan_start)
self.ui.scan_stop_pushButton.clicked.connect(self.on_scan_stop)
self.ui.fast_update_checkBox.stateChanged.connect(self.on_fast_timer_checkbox)
self.ui.clearfig_pushButton.clicked.connect(self.on_clearfig)
### timers
self.timer = QtCore.QTimer(self.ui)
self.timer.timeout.connect(self.on_timer)
self.timer.start(TIMER_MS)
self.fast_timer = QtCore.QTimer(self.ui)
self.fast_timer.timeout.connect(self.on_fast_timer)
self.display_update_when_scanning_timer = QtCore.QTimer(self.ui)
self.display_update_when_scanning_timer.timeout.connect(self.on_display_update_when_scanning_timer)
class ScanningConfocalUI:
def __del__ ( self ):
self.ui = None
def show(self):
#self.ui.exec_()
self.ui.show()
def __init__(self):
ui_loader = QtUiTools.QUiLoader()
print os.path.join(__file__,"scanning_confocal_mcl_lj.ui")
ui_file = QtCore.QFile("scanning_confocal_mcl_lj.ui")
ui_file.open(QtCore.QFile.ReadOnly);
self.ui = ui_loader.load(ui_file)
ui_file.close()
self.HARDWARE_DEBUG = HARDWARE_DEBUG
self.fig2d = Figure()
self.ax2d = self.fig2d.add_subplot(111)
self.ax2d.plot([0,1])
self.canvas2d = FigureCanvas(self.fig2d)
self.ui.plot2D_verticalLayout.addWidget(self.canvas2d)
self.navtoolbar_plot2d = NavigationToolbar2(self.canvas2d, self.ui)
self.ui.plot2D_verticalLayout.addWidget( self.navtoolbar_plot2d )
self.fig_opt = Figure()
self.ax_opt = self.fig_opt.add_subplot(111)
self.canvas_opt = FigureCanvas(self.fig_opt)
self.ui.plot_optimize_verticalLayout.addWidget(self.canvas_opt)
self.navtoolbar_plot_opt = NavigationToolbar2(self.canvas_opt, self.ui)
self.ui.plot_optimize_verticalLayout.addWidget( self.navtoolbar_plot_opt )
self.optimize_history = np.zeros(OPTIMIZE_HISTORY_LEN, dtype=np.float)
self.optimize_ii = 0
self.optimize_line, = self.ax_opt.plot(self.optimize_history)
self.optimize_current_pos = self.ax_opt.axvline(self.optimize_ii, color='r')
##################### hardware #########################################
self.scanning = False
######## MCL NanoDrive Stage ###########################################
self.nanodrive = MCLNanoDrive(debug=self.HARDWARE_DEBUG)
try:
self.hmax = self.nanodrive.cal[HAXIS_ID]
self.vmax = self.nanodrive.cal[VAXIS_ID]
self.ui.maxdim_label.setText("max: %g x %g um" % (self.hmax, self.vmax) )
except Exception as e:
print e
self.ui.maxdim_label.setText("max: ? x ? um")
# Logged Quantities
self.x_position = LoggedQuantity(name = 'x_position', dtype=np.float)
self.y_position = LoggedQuantity(name = 'y_position', dtype=np.float)
self.z_position = LoggedQuantity(name = 'z_position', dtype=np.float)
#self.x_position.updated_value.connect(self.ui.cx_lcdNumber.display)
self.x_position.updated_value.connect(self.ui.cx_doubleSpinBox.setValue)
self.ui.x_set_lineEdit.returnPressed.connect(self.x_position.update_value)
#self.y_position.updated_value.connect(self.ui.cy_lcdNumber.display)
self.y_position.updated_value.connect(self.ui.cy_doubleSpinBox.setValue)
self.ui.y_set_lineEdit.returnPressed.connect(self.y_position.update_value)
#self.z_position.updated_value.connect(self.ui.cz_lcdNumber.display)
self.z_position.updated_value.connect(self.ui.cz_doubleSpinBox.setValue)
self.ui.z_set_lineEdit.returnPressed.connect(self.z_position.update_value)
self.x_position.hardware_set_func = lambda x: self.nanodrive.set_pos_ax(x, XAXIS_ID)
self.y_position.hardware_set_func = lambda y: self.nanodrive.set_pos_ax(y, YAXIS_ID)
self.z_position.hardware_set_func = lambda z: self.nanodrive.set_pos_ax(z, ZAXIS_ID)
####### LabJack (apd) counter readout ##################################
self.lj_counter = labjack_counter.LabJackCounter()
self.apd_count_rate = LoggedQuantity(name = 'apd_count_rate', dtype=np.float, fmt="%e")
self.apd_count_rate.updated_text_value.connect(self.ui.apd_counter_output_lineEdit.setText)
########################################################################
self.read_from_hardware()
self.update_display()
# update figure
self.ax2d.set_xlim(0, self.hmax)
self.ax2d.set_ylim(0, self.vmax)
# events
self.ui.scan_start_pushButton.clicked.connect(self.on_scan_start)
self.ui.scan_stop_pushButton.clicked.connect(self.on_scan_stop)
self.ui.fast_update_checkBox.stateChanged.connect(self.on_fast_timer_checkbox)
self.ui.clearfig_pushButton.clicked.connect(self.on_clearfig)
### timers
self.timer = QtCore.QTimer(self.ui)
self.timer.timeout.connect(self.on_timer)
self.timer.start(TIMER_MS)
self.fast_timer = QtCore.QTimer(self.ui)
self.fast_timer.timeout.connect(self.on_fast_timer)
self.display_update_when_scanning_timer = QtCore.QTimer(self.ui)
self.display_update_when_scanning_timer.timeout.connect(self.on_display_update_when_scanning_timer)
@QtCore.Slot()
def on_clearfig(self):
self.fig2d.clf()
self.ax2d = self.fig2d.add_subplot(111)
self.ax2d.plot([0,1])
# update figure
self.ax2d.set_xlim(0, self.hmax)
self.ax2d.set_ylim(0, self.vmax)
self.fig2d.canvas.draw()
def read_from_hardware(self):
self.stage_pos = self.nanodrive.get_pos()
self.c0_rate = self.lj_counter.read_rates()[0]
def update_display(self):
self.x_position.update_value(self.stage_pos[XAXIS_ID-1], update_hardware=False)
self.y_position.update_value(self.stage_pos[YAXIS_ID-1], update_hardware=False)
self.z_position.update_value(self.stage_pos[ZAXIS_ID-1], update_hardware=False)
self.apd_count_rate.update_value(self.c0_rate)
@QtCore.Slot()
def on_timer(self):
self.read_from_hardware()
self.update_display()
@QtCore.Slot()
def on_fast_timer(self):
self.c0_rate = self.lj_counter.read_rates()[0]
self.apd_count_rate.update_value(self.c0_rate)
#print self.c0_rate
self.optimize_ii += 1
self.optimize_ii %= OPTIMIZE_HISTORY_LEN
ii = self.optimize_ii
self.optimize_history[ii] = self.c0_rate
self.optimize_line.set_ydata(self.optimize_history)
self.optimize_current_pos.set_xdata((ii,ii))
if (ii % 10) == 0:
self.ax_opt.relim()
self.ax_opt.autoscale_view(scalex=False, scaley=True)
#print "redraw"
self.fig_opt.canvas.draw()
@QtCore.Slot(bool)
def on_fast_timer_checkbox(self, fast_timer_enable):
if fast_timer_enable:
self.fast_timer.start(100)
print "fast timer start"
else:
self.fast_timer.stop()
print "fast timer stop"
@QtCore.Slot()
def on_scan_start(self):
print "start scan"
self.scanning = True
QtGui.QApplication.processEvents()
#get scan parameters:
self.h0 = self.ui.h0_doubleSpinBox.value()
self.h1 = self.ui.h1_doubleSpinBox.value()
self.v0 = self.ui.v0_doubleSpinBox.value()
self.v1 = self.ui.v1_doubleSpinBox.value()
self.dh = 1e-3*self.ui.dh_spinBox.value()
self.dv = 1e-3*self.ui.dv_spinBox.value()
self.h_array = np.arange(self.h0, self.h1, self.dh, dtype=float)
self.v_array = np.arange(self.v0, self.v1, self.dv, dtype=float)
self.Nh = len(self.h_array)
self.Nv = len(self.v_array)
self.pixel_time = self.ui.pixel_time_doubleSpinBox.value()
### create data arrays
self.count_rate_map = np.zeros((self.Nv, self.Nh), dtype=np.float)
print "shape:", self.count_rate_map.shape
print "Nh, Nv", self.Nh, self.Nv
### update figure
self.ax_2d_img = self.ax2d.imshow(self.count_rate_map,
origin='lower',
vmin=1e4, vmax=1e5, interpolation='nearest',
extent=[self.h0, self.h1, self.v0, self.v1])
self.fig2d.canvas.draw()
self.timer.stop() #stop the normal timer
#display_timer_update = 0.5*self.pixel_time*1e3
#if display_timer_update < 200
self.display_update_when_scanning_timer.start(100)
# Scan!
line_time0 = time.time()
for i_v in range(self.Nv):
if not self.scanning:
break
self.v_pos = self.v_array[i_v]
self.nanodrive.set_pos_ax(self.v_pos, VAXIS_ID)
self.read_from_hardware()
print "line time:", time.time() - line_time0
print "pixel time:", float(time.time() - line_time0)/self.Nh
line_time0 = time.time()
if i_v % 2: #odd lines
h_line_indicies = range(self.Nh)
else: #even lines -- traverse in oposite direction
h_line_indicies = range(self.Nh)[::-1]
for i_h in h_line_indicies:
if not self.scanning:
break
self.h_pos = self.h_array[i_h]
self.nanodrive.set_pos_ax(self.h_pos, XAXIS_ID)
time0 = time.time()
while time.time() - time0 < self.pixel_time:
QtGui.QApplication.processEvents() #release
counts = self.lj_counter.read_rates()
#self.count_rate_map[i_v,i_h] = counts[-1] # grab integration time for now
self.c0_rate = counts[0]
self.count_rate_map[i_v,i_h] = self.c0_rate # grab count0 rate
"""self.ccd.start_acquisition()
stat = "ACQUIRING"
while stat!= "IDLE":
wx_yielded_sleep(self.ccd.exposure_time * 0.25)
stati, stat = self.ccd.get_status()
self.ccd.get_acquired_data()
spectrum = np.sum(self.ccd.buffer[ROW0:ROW1], axis=0)
self.spectrum_map[jj,ii,:] = spectrum
self.integrated_count_map[jj,ii] = sum(spectrum)
"""
self.on_scan_stop()
@QtCore.Slot()
def on_scan_stop(self):
print "on_scan_stop"
self.scanning = False
self.update_display()
self.timer.start() #restart the normal timer
self.display_update_when_scanning_timer.stop()
# clean up after scan
self.ax_2d_img.set_data(self.count_rate_map)
self.fig2d.canvas.draw()
self.update_display()
self.scanning = False
print "scanning done"
"""
print "saving data..."
t0 = time.time()
#np.savetxt("%i_confocal_scan.csv" % t0,
# self.integrated_count_map, delimiter=',')
save_params = ["spectrum_map", "x0", "x1", "y0", "y1",
"Nx", "Ny",
"x_array", "y_array",
"dx", "dy", "integrated_count_map"]
save_dict = dict()
for key in save_params:
save_dict[key] = getattr(self, key)
for key in ["XAXIS_ID", "YAXIS_ID","HARDWARE_DEBUG","ANDOR_HFLIP","ANDOR_VFLIP","ANDOR_AD_CHAN","ROW0","ROW1"]:
save_dict[key] = globals()[key]
for key in ["wl", "gratings", "grating"]:
save_dict["spec_"+key] = getattr(self.spec, key)
for key in ["exposure_time", "em_gain", "temperature", "ad_chan", "ro_mode", "Nx", "Ny"]:
save_dict["andor_"+key] = getattr(self.ccd, key)
save_dict["time_saved"] = t0
np.savez_compressed("%i_spec_map.npz" % t0, **save_dict)
print "data saved"
"""
@QtCore.Slot()
def on_display_update_when_scanning_timer(self):
# update display
try:
self.update_display()
except Exception, err:
print "Failed to update_display", err
try:
#self.spec_plotline.set_ydata(spectrum)
#self.ax_speclive.relim()
#self.ax_speclive.autoscale_view(tight=None, scalex=False, scaley=True)
#self.fig2.canvas.draw()
pass
except Exception as err:
print "Failed to update spectrum plot", err
try:
#print "updating figure"
#self.read_from_hardware()
self.ax_2d_img.set_data(self.count_rate_map)
try:
count_min = np.min(self.count_rate_map[np.nonzero(self.count_rate_map)])
except Exception as err:
count_min = 0
count_max = np.max(self.count_rate_map)
self.ax_2d_img.set_clim(count_min, count_max + 1)
self.fig2d.canvas.draw()
except Exception, err:
print "Failed to update figure:", err