def scp(global_PVs, variableDict):
log_lib.info(' ')
log_lib.info(' *** Data transfer')
remote_server = variableDict['RemoteAnalysisDir'].split(':')[0]
remote_top_dir = variableDict['RemoteAnalysisDir'].split(':')[1]
log_lib.info(' *** remote server: %s' % remote_server)
log_lib.info(' *** remote top directory: %s' % remote_top_dir)
fname_origin = global_PVs['HDF1_FullFileName_RBV'].get(as_string=True)
p = pathlib.Path(fname_origin)
fname_destination = variableDict['RemoteAnalysisDir'] + p.parts[
-3] + '/' + p.parts[-2] + '/'
remote_dir = remote_top_dir + p.parts[-3] + '/' + p.parts[-2] + '/'
log_lib.info(' *** origin: %s' % fname_origin)
log_lib.info(' *** destination: %s' % fname_destination)
# log_lib.info(' *** remote directory: %s' % remote_dir)
ret = check_remote_directory(remote_server, remote_dir)
if ret == 0:
os.system('scp -q ' + fname_origin + ' ' + fname_destination + '&')
log_lib.info(' *** Data transfer: Done!')
return 0
elif ret == 2:
iret = create_remote_directory(remote_server, remote_dir)
if iret == 0:
os.system('scp -q ' + fname_origin + ' ' + fname_destination + '&')
log_lib.info(' *** Data transfer: Done!')
return 0
else:
log_lib.error(' *** Quitting the copy operation')
return -1
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
# moved pgInit() here from tomo_fly_scan()
aps2bm_lib.pgInit(global_PVs, variableDict)
# get sample file name
fname = global_PVs['HDF1_FileName'].get(as_string=True)
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!')
scan_lib.dummy_tomo_fly_scan(global_PVs, variableDict, fname)
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))
log_lib.info(' *** Done!')
except KeyError:
log_lib.error(' *** Some PV assignment failed!')
pass
def create_remote_directory(remote_server, remote_dir):
cmd = 'mkdir -p ' + remote_dir
try:
# log_lib.info(' *** sending command %s' % (cmd))
log_lib.info(' *** creating remote directory %s' % (remote_dir))
subprocess.check_call(['ssh', remote_server, cmd])
log_lib.info(' *** creating remote directory %s: Done!' %
(remote_dir))
return 0
except subprocess.CalledProcessError, e:
log_lib.error(
' *** Error while creating remote directory. Error code: %d' %
(e.returncode))
return -1
def check_remote_directory(remote_server, remote_dir):
try:
rcmd = 'ls ' + remote_dir
# rcmd is the command used to check if the remote directory exists
subprocess.check_call(['ssh', remote_server, rcmd],
stderr=open(os.devnull, 'wb'),
stdout=open(os.devnull, 'wb'))
log_lib.warning(' *** remote directory %s exists' % (remote_dir))
return 0
except subprocess.CalledProcessError, e:
# log_lib.info(' *** return code = %d' % (e.returncode))
log_lib.warning(' *** remote directory %s does not exist' %
(remote_dir))
if e.returncode == 2:
return e.returncode
else:
log_lib.error(' *** Unknown error code returned: %d' %
(e.returncode))
return -1
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
