def main():
# create logger
# # python 3.5+
# home = str(pathlib.Path.home())
home = os.path.expanduser("~")
logs_home = home + '/logs/'
# make sure logs directory exists
if not os.path.exists(logs_home):
os.makedirs(logs_home)
lfname = logs_home + datetime.strftime(datetime.now(),
"%Y-%m-%d_%H:%M:%S") + '.log'
log_lib.setup_logger(lfname)
tic = time.time()
aps32id_lib.update_variable_dict(variableDict)
aps32id_lib.init_general_PVs(global_PVs, variableDict)
FileName = global_PVs['HDF1_FileName'].get(as_string=True)
nLoops = variableDict['nLoops']
# global_PVs['HDF1_NextFile'].put(0)
for iLoop in range(0, nLoops):
log_lib.info(' ')
log_lib.info(' *** Starting step scan #%i' % (iLoop + 1))
global_PVs['Motor_SampleRot'].put(variableDict['SampleStart_Rot'],
wait=True,
timeout=600.0)
scan_lib.tomo_step_scan(variableDict, global_PVs, FileName)
dm_lib.scp(global_PVs, variableDict)
log_lib.info(' ')
log_lib.info(' *** Total scan time: %.2f minutes' %
((time.time() - tic) / 60.))
def main():
# create logger
# # python 3.5+
# home = str(pathlib.Path.home())
home = os.path.expanduser("~")
logs_home = home + '/logs/'
# make sure logs directory exists
if not os.path.exists(logs_home):
os.makedirs(logs_home)
lfname = logs_home + datetime.strftime(datetime.now(),
"%Y-%m-%d_%H:%M:%S") + '.log'
log_lib.setup_logger(lfname)
aps32id_lib.update_variable_dict(variableDict)
aps32id_lib.init_general_PVs(global_PVs, variableDict)
FileName = global_PVs['TIFF1_FileName'].get(as_string=True)
log_lib.info(' ')
log_lib.info(' *** Starting tiff stack acq.')
scan_lib.tiff_2Dscan(variableDict, global_PVs, FileName)
dm_lib.scp(global_PVs, variableDict)
def main():
# create logger
# # python 3.5+
# home = str(pathlib.Path.home())
home = os.path.expanduser("~")
logs_home = home + '/logs/'
# make sure logs directory exists
if not os.path.exists(logs_home):
os.makedirs(logs_home)
lfname = logs_home + datetime.strftime(datetime.now(), "%Y-%m-%d_%H:%M:%S") + '.log'
log_lib.setup_logger(lfname)
tic = time.time()
aps2bm_lib.update_variable_dict(variableDict)
aps2bm_lib.init_general_PVs(global_PVs, variableDict)
try:
detector_sn = global_PVs['Cam1_SerialNumber'].get()
if ((detector_sn == None) or (detector_sn == 'Unknown')):
log_lib.error('*** The Point Grey Camera with EPICS IOC prefix %s is down' % variableDict['IOC_Prefix'])
log_lib.error(' *** Failed!')
else:
log_lib.info('*** The Point Grey Camera with EPICS IOC prefix %s and serial number %s is on' \
% (variableDict['IOC_Prefix'], detector_sn))
# calling global_PVs['Cam1_AcquireTime'] to replace the default 'ExposureTime' with the one set in the camera
variableDict['ExposureTime'] = global_PVs['Cam1_AcquireTime'].get()
# calling calc_blur_pixel() to replace the default 'SlewSpeed'
blur_pixel, rot_speed, scan_time = aps2bm_lib.calc_blur_pixel(global_PVs, variableDict)
variableDict['SlewSpeed'] = rot_speed
# start = variableDict['SleepStart']
# end = variableDict['SleepEnd']
# step_size = variableDict['SleepStep']
start = 0
end = variableDict['SleepStep']
step_size = 1
# init camera
aps2bm_lib.pgInit(global_PVs, variableDict)
log_lib.info(' ')
log_lib.info(" *** Running %d scans" % len(np.arange(start, end, step_size)))
for i in np.arange(start, end, step_size):
tic_01 = time.time()
fname = str('{:03}'.format(global_PVs['HDF1_FileNumber'].get())) + '_' + global_PVs['Sample_Name'].get(as_string=True)
log_lib.info(' ')
log_lib.info(' *** Start scan %d' % i)
scan_lib.tomo_fly_scan(global_PVs, variableDict, fname)
if ((i+1)!=end):
log_lib.warning(' *** Wait (s): %s ' % str(variableDict['SleepTime_s']))
time.sleep(variableDict['SleepTime_s'])
log_lib.info(' ')
log_lib.info(' *** Data file: %s' % global_PVs['HDF1_FullFileName_RBV'].get(as_string=True))
log_lib.info(' *** Total scan time: %s minutes' % str((time.time() - tic_01)/60.))
log_lib.info(' *** Scan Done!')
dm_lib.scp(global_PVs, variableDict)
log_lib.info(' *** Total loop scan time: %s minutes' % str((time.time() - tic)/60.))
log_lib.info(' *** Moving rotary stage to start position')
global_PVs["Motor_SampleRot"].put(0, wait=True, timeout=600.0)
log_lib.info(' *** Moving rotary stage to start position: Done!')
global_PVs['Cam1_ImageMode'].put('Continuous')
log_lib.info(' *** Done!')
except KeyError:
log_lib.error(' *** Some PV assignment failed!')
pass
def main():
# create logger
# # python 3.5+
# home = str(pathlib.Path.home())
home = os.path.expanduser("~")
logs_home = home + '/logs/'
# make sure logs directory exists
if not os.path.exists(logs_home):
os.makedirs(logs_home)
lfname = logs_home + datetime.strftime(datetime.now(),
"%Y-%m-%d_%H:%M:%S") + '.log'
log_lib.setup_logger(lfname)
tic = time.time()
aps2bm_lib.update_variable_dict(variableDict)
aps2bm_lib.init_general_PVs(global_PVs, variableDict)
try:
detector_sn = global_PVs['Cam1_SerialNumber'].get()
if ((detector_sn == None) or (detector_sn == 'Unknown')):
log_lib.info(
'*** The Point Grey Camera with EPICS IOC prefix %s is down' %
variableDict['IOC_Prefix'])
log_lib.info(' *** Failed!')
else:
log_lib.info('*** The Point Grey Camera with EPICS IOC prefix %s and serial number %s is on' \
% (variableDict['IOC_Prefix'], detector_sn))
# calling global_PVs['Cam1_AcquireTime'] to replace the default 'ExposureTime' with the one set in the camera
variableDict['ExposureTime'] = global_PVs['Cam1_AcquireTime'].get()
# calling calc_blur_pixel() to replace the default 'SlewSpeed'
blur_pixel, rot_speed, scan_time = aps2bm_lib.calc_blur_pixel(
global_PVs, variableDict)
variableDict['SlewSpeed'] = rot_speed
start_y = variableDict['StartY']
end_y = variableDict['EndY']
step_size_y = variableDict['StepSizeY']
start_x = variableDict['StartX']
end_x = variableDict['EndX']
step_size_x = variableDict['StepSizeX']
# set scan stop so also ends are included
stop_x = end_x + step_size_x
stop_y = end_y + step_size_y
# init camera
aps2bm_lib.pgInit(global_PVs, variableDict)
start = variableDict['SleepStart']
end = variableDict['SleepEnd']
step_size = variableDict['SleepStep']
log_lib.info(' ')
log_lib.info(" *** Running %d sleep scans" %
len(np.arange(start, end, step_size)))
for ii in np.arange(start, end, step_size):
tic_01 = time.time()
log_lib.info(' ')
log_lib.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_lib.info(' ')
log_lib.info(' *** Horizontal Positions (mm): %s' %
np.arange(start_x, stop_x, step_size_x))
log_lib.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_lib.info(' ')
log_lib.info(
' *** 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_lib.info(
' *** The sample horizontal position is at %s mm'
% (j))
variableDict['SampleXIn'] = j
fname = str('{:03}'.format(
global_PVs['HDF1_FileNumber'].get(
))) + '_' + global_PVs['Sample_Name'].get(
as_string=True) + '_y' + str(v) + '_x' + str(h)
scan_lib.tomo_fly_scan(global_PVs, variableDict, fname)
h = h + 1
dm_lib.scp(global_PVs, variableDict)
log_lib.info(' ')
log_lib.info(' *** Total scan time: %s minutes' % str(
(time.time() - tic) / 60.))
log_lib.info(' *** Data file: %s' %
global_PVs['HDF1_FullFileName_RBV'].get(
as_string=True))
v = v + 1
h = 0
log_lib.info(' *** Moving rotary stage to start position')
global_PVs["Motor_SampleRot"].put(0, wait=True, timeout=600.0)
log_lib.info(
' *** Moving rotary stage to start position: Done!')
if ((ii + 1) != end):
log_lib.warning(' *** Wait (s): %s ' %
str(variableDict['SleepTime']))
time.sleep(variableDict['SleepTime'])
global_PVs['Cam1_ImageMode'].put('Continuous')
log_lib.info(' *** Done!')
except KeyError:
log_lib.error(' *** Some PV assignment failed!')
pass