def fly_scan(params):
tic = time.time()
global_PVs = aps2bm.init_general_PVs(params)
aps2bm.user_info_params_update_from_pv(global_PVs, params)
try:
detector_sn = global_PVs['Cam1_SerialNumber'].get()
if ((detector_sn == None) or (detector_sn == 'Unknown')):
log.info('*** The Point Grey Camera with EPICS IOC prefix %s is down' % params.camera_ioc_prefix)
log.info(' *** Failed!')
else:
log.info('*** The Point Grey Camera with EPICS IOC prefix %s and serial number %s is on' \
% (params.camera_ioc_prefix, detector_sn))
# calling global_PVs['Cam1_AcquireTime'] to replace the default 'ExposureTime' with the one set in the camera
params.exposure_time = global_PVs['Cam1_AcquireTime'].get()
# calling calc_blur_pixel() to replace the default 'SlewSpeed'
rot_speed = calc_blur_pixel(global_PVs, params)
params.slew_speed = rot_speed
# init camera
flir.init(global_PVs, params)
log.info(' ')
log.info(" *** Running %d sleep scans" % params.sleep_steps)
for i in np.arange(0, params.sleep_steps, 1):
tic_01 = time.time()
# set sample file name
#fname = str('{:03}'.format(global_PVs['HDF1_FileNumber'].get())) + '_' + global_PVs['Sample_Name'].get(as_string=True)
params.scan_counter = global_PVs['HDF1_FileNumber'].get()
params.file_path = global_PVs['HDF1_FilePath'].get(as_string=True)
params.file_name = str('{:03}'.format(global_PVs['HDF1_FileNumber'].get())) + '_' + global_PVs['Sample_Name'].get(as_string=True)
log.info(' ')
log.info(' *** Start scan %d/%d' % (i, (params.sleep_steps -1)))
tomo_fly_scan(global_PVs, params)
if ((i+1)!= params.sleep_steps):
log.warning(' *** Wait (s): %s ' % str(params.sleep_time))
time.sleep(params.sleep_time)
log.info(' ')
log.info(' *** Data file: %s' % global_PVs['HDF1_FullFileName_RBV'].get(as_string=True))
log.info(' *** Total scan time: %s minutes' % str((time.time() - tic_01)/60.))
log.info(' *** Scan Done!')
dm.scp(global_PVs, params)
log.info(' *** Total loop scan time: %s minutes' % str((time.time() - tic)/60.))
log.info(' *** Moving rotary stage to start position')
global_PVs["Motor_SampleRot"].put(params.sample_rotation_start, wait=True, timeout=600.0)
log.info(' *** Moving rotary stage to start position: Done!')
global_PVs['Cam1_ImageMode'].put('Continuous')
log.info(' *** Done!')
except KeyError:
log.error(' *** Some PV assignment failed!')
pass
def stop_scan(global_PVs, params):
log.info(' ')
log.error(' *** Stopping the scan: PLEASE WAIT')
global_PVs['Motor_SampleRot_Stop'].put(1)
global_PVs['HDF1_Capture'].put(0)
aps2bm.wait_pv(global_PVs['HDF1_Capture'], 0)
flir.init(global_PVs, params)
log.error(' *** Stopping scan: Done!')
def adjust(params):
global_PVs = aps2bm.init_general_PVs(params)
params.file_name = None # so we don't run the flir._setup_hdf_writer
try:
detector_sn = global_PVs['Cam1_SerialNumber'].get()
if ((detector_sn == None) or (detector_sn == 'Unknown')):
log.info(
'*** The Point Grey Camera with EPICS IOC prefix %s is down' %
params.camera_ioc_prefix)
log.info(' *** Failed!')
else:
log.info('*** The Point Grey Camera with EPICS IOC prefix %s and serial number %s is on' \
% (params.camera_ioc_prefix, detector_sn))
flir.init(global_PVs, params)
flir.set(global_PVs, params)
dark_field, white_field = flir.take_dark_and_white(
global_PVs, params)
if (params.resolution == True):
find_resolution(params,
dark_field,
white_field,
angle_shift=-0.7)
if (params.image_resolution == None):
log.error(
' *** Detector resolution is not determined. Please run tomo adjust --resolution first!'
)
exit()
else:
if (params.focus == True):
adjust_focus(params)
if (params.center == True):
adjust_center(params, dark_field, white_field)
if (params.roll == True):
adjust_roll(params,
dark_field,
white_field,
angle_shift=-0.7)
if (params.pitch == True):
adjust_pitch(params,
dark_field,
white_field,
angle_shift=-0.7)
if (params.roll == True or params.pitch == True):
# align center again for higher accuracy
adjust_center(params, dark_field, white_field)
config.update_sphere(params)
except KeyError:
log.error(' *** Some PV assignment failed!')
pass
def fly_scan_mosaic(params):
tic = time.time()
global_PVs = aps2bm.init_general_PVs(params)
aps2bm.user_info_params_update_from_pv(global_PVs, params)
try:
detector_sn = global_PVs['Cam1_SerialNumber'].get()
if ((detector_sn == None) or (detector_sn == 'Unknown')):
log.info('*** The Point Grey Camera with EPICS IOC prefix %s is down' % params.camera_ioc_prefix)
log.info(' *** Failed!')
else:
log.info('*** The Point Grey Camera with EPICS IOC prefix %s and serial number %s is on' \
% (params.camera_ioc_prefix, detector_sn))
# calling global_PVs['Cam1_AcquireTime'] to replace the default 'ExposureTime' with the one set in the camera
params.exposure_time = global_PVs['Cam1_AcquireTime'].get()
# calling calc_blur_pixel() to replace the default 'SlewSpeed'
rot_speed = calc_blur_pixel(global_PVs, params)
params.slew_speed = rot_speed
start_y = params.vertical_scan_start
end_y = params.vertical_scan_end
step_size_y = params.vertical_scan_step_size
start_x = params.horizontal_scan_start
end_x = params.horizontal_scan_end
step_size_x = params.horizontal_scan_step_size
# set scan stop so also ends are included
stop_x = end_x + step_size_x
stop_y = end_y + step_size_y
# init camera
flir.init(global_PVs, params)
log.info(' ')
log.info(" *** Running %d sleep scans" % params.sleep_steps)
for ii in np.arange(0, params.sleep_steps, 1):
tic_01 = time.time()
log.info(' ')
log.info(" *** Running %d mosaic scans" % (len(np.arange(start_x, stop_x, step_size_x)) * len(np.arange(start_y, stop_y, step_size_y))))
log.info(' ')
log.info(' *** Horizontal Positions (mm): %s' % np.arange(start_x, stop_x, step_size_x))
log.info(' *** Vertical Positions (mm): %s' % np.arange(start_y, stop_y, step_size_y))
h = 0
v = 0
for i in np.arange(start_y, stop_y, step_size_y):
log.info(' ')
log.error(' *** The sample vertical position is at %s mm' % (i))
global_PVs['Motor_SampleY'].put(i, wait=True)
for j in np.arange(start_x, stop_x, step_size_x):
log.error(' *** The sample horizontal position is at %s mm' % (j))
params.sample_in_position = j
params.scan_counter = global_PVs['HDF1_FileNumber'].get()
# set sample file name
params.file_path = global_PVs['HDF1_FilePath'].get(as_string=True)
params.file_name = str('{:03}'.format(global_PVs['HDF1_FileNumber'].get())) + '_' + global_PVs['Sample_Name'].get(as_string=True) + '_y' + str(v) + '_x' + str(h)
tomo_fly_scan(global_PVs, params)
h = h + 1
dm.scp(global_PVs, params)
log.info(' ')
log.info(' *** Total scan time: %s minutes' % str((time.time() - tic)/60.))
log.info(' *** Data file: %s' % global_PVs['HDF1_FullFileName_RBV'].get(as_string=True))
v = v + 1
h = 0
log.info(' *** Moving vertical stage to start position')
global_PVs['Motor_SampleY'].put(start_y, wait=True, timeout=1000.0)
log.info(' *** Moving horizontal stage to start position')
global_PVs['Motor_SampleX'].put(start_x, wait=True, timeout=1000.0)
log.info(' *** Moving rotary stage to start position')
global_PVs["Motor_SampleRot"].put(params.sample_rotation_start, wait=True, timeout=600.0)
log.info(' *** Moving rotary stage to start position: Done!')
if ((ii+1)!=params.sleep_steps):
log.warning(' *** Wait (s): %s ' % str(params.sleep_time))
time.sleep(params.sleep_time)
global_PVs['Cam1_ImageMode'].put('Continuous')
log.info(' *** Done!')
except KeyError:
log.error(' *** Some PV assignment failed!')
pass