def pre_scan_setup(self):
IRMicroscopeBase2DScan.pre_scan_setup(self)
# Based on winspec_readout measurement
self.ccd_measure.interrupt()
#Reconnect to winspec (Clears Server Buffer)
self.ccd_measure.winspec_hc.settings['connected'] = False
time.sleep(0.2)
self.ccd_measure.winspec_hc.settings['connected'] = True
time.sleep(0.2)
# Setup data structures
self.map_shape = (*self.scan_shape, 1024)
self.px_index = np.arange(self.map_shape[-1])
self.wls = self.px_index
if self.settings['save_h5']:
self.hyperspectral_map_h5 = self.h5_meas_group.create_dataset(
'hyperspectral_map',
shape=self.map_shape,
dtype=float,
compression='gzip')
self.integrated_count_map_h5 = self.h5_meas_group.create_dataset(
'integrated_count_map',
shape=self.scan_shape,
dtype=float,
compression='gzip')
self.wls_h5 = self.h5_meas_group.create_dataset('wls',
shape=(1024, ),
dtype=float,
compression='gzip')
def setup_figure(self):
IRMicroscopeBase2DScan.setup_figure(self)
self.graph_layout.nextRow()
self.spec_plot = self.graph_layout.addPlot(title='Current Spectrum',
left='Intensity',
bottom='Wavelength (nm)')
self.spec_plot_line = self.spec_plot.plot([1, 3, 2, 4, 3, 5])
def collect_pixel(self, pixel_num, k, j, i):
self.ccd_measure.interrupt_measurement_called = self.interrupt_measurement_called
IRMicroscopeBase2DScan.collect_pixel(self, pixel_num, k, j, i)
#calculate time remaining, there is almost 0.72 second overhead per pixel.
#sec_remaining = (self.Npixels-(pixel_num+1))*(self.app.hardware['winspec_remote_client'].settings['acq_time']+0.72)
#print(self.name, "collecting pixel: (",k,j,i, ") number:", pixel_num+1,"of",self.Npixels,
# 'estimated time remaining:',datetime.timedelta(seconds=sec_remaining) )
#acquire ccd data
counter = 0
retry = True
while (retry):
try:
counter += 1
hdr, data = self.ccd_measure.acquire_data(debug=False)
#1print(counter)
retry = False
except:
print('An error occurred while aquire_data(), try', counter,
'/4')
retry = True
finally:
if counter > 3:
retry = False
#self.measurement_sucessfully_completed = False
if hdr is None or data is None:
raise IOError("Failed to acquire Data (probably interrupted)")
self.hdr = hdr
self.data = data[0, 0, :]
if pixel_num == 0:
self.wls = self.ccd_measure.evaluate_wls_acton_spectrometer(
self.hdr, self.px_index)
intensity = self.data.sum()
self.display_image_map[k, j, i] = intensity
# save spectral data
if self.settings['save_h5']:
self.hyperspectral_map_h5[k, j, i, :] = self.data
self.integrated_count_map_h5[k, j, i] = intensity
if pixel_num == 0:
self.wls_h5[:] = self.wls
def pre_run(self):
IRMicroscopeBase2DScan.pre_run(self)
self.ccd_measure.pre_run()
def setup(self):
IRMicroscopeBase2DScan.setup(self)
#print(self.name, "setup() called")
self.ccd_measure = self.app.measurements['winspec_readout']
def __init__(self, app):
IRMicroscopeBase2DScan.__init__(self, app)
def update_display(self):
IRMicroscopeBase2DScan.update_display(self)
def collect_pixel(self, pixel_num, k, j, i):
IRMicroscopeBase2DScan.collect_pixel(self, pixel_num, k, j, i)
AndorHyperSpec2DScanBase.collect_pixel(self, pixel_num, k, j, i)
def setup(self):
IRMicroscopeBase2DScan.setup(self)
TRPL2DScanBase.setup(self)
def pre_scan_setup(self):
AndorHyperSpec2DScanBase.pre_scan_setup(self)
IRMicroscopeBase2DScan.pre_scan_setup(self)
def update_display(self):
if not hasattr(self, 'data'):
return
self.spec_plot_line.setData(self.wls, self.data)
IRMicroscopeBase2DScan.update_display(self)
def setup(self):
IRMicroscopeBase2DScan.setup(self)
def post_scan_cleanup(self):
IRMicroscopeBase2DScan.post_scan_cleanup(self)
TRPL2DScanBase.post_scan_cleanup(self)
def collect_pixel(self, pixel_num, k, j, i):
IRMicroscopeBase2DScan.collect_pixel(self, pixel_num, k, j, i)
TRPL2DScanBase.collect_pixel(self, pixel_num, k, j, i)
def pre_scan_setup(self):
IRMicroscopeBase2DScan.pre_scan_setup(self)
TRPL2DScanBase.pre_scan_setup(self)
def setup_figure(self):
TRPL2DScanBase.setup_figure(self)
IRMicroscopeBase2DScan.setup_figure(self)
def post_scan_cleanup(self):
AndorHyperSpec2DScanBase.post_scan_cleanup(self)
IRMicroscopeBase2DScan.post_scan_cleanup(self)
def __init__(self, app):
IRMicroscopeBase2DScan.__init__(self, app)
TRPL2DScanBase.__init__(self, app, None)
