def wait_pv(pv, wait_val, max_timeout_sec=-1):
# wait on a pv to be a value until max_timeout (default forever)
# delay for pv to change
time.sleep(.01)
startTime = time.time()
while (True):
pv_val = pv.get()
if type(pv_val) == float:
if abs(pv_val - wait_val) < EPSILON:
return True
if (pv_val != wait_val):
if max_timeout_sec > -1:
curTime = time.time()
diffTime = curTime - startTime
if diffTime >= max_timeout_sec:
log.error(' *** ERROR: DROPPED IMAGES ***')
log.error(
' *** wait_pv(%s, %d, %5.2f reached max timeout. Return False'
% (pv.pvname, wait_val, max_timeout_sec))
return False
time.sleep(.01)
else:
return True
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 scp(global_PVs, params):
log.info(' ')
log.info(' *** Data transfer')
remote_server = params.remote_analysis_dir.split(':')[0]
remote_top_dir = params.remote_analysis_dir.split(':')[1]
log.info(' *** remote server: %s' % remote_server)
log.info(' *** remote top directory: %s' % remote_top_dir)
fname_origin = global_PVs['HDFFullFileName_RBV'].get(as_string=True)
p = pathlib.Path(fname_origin)
fname_destination = params.remote_analysis_dir + p.parts[-3] + '/' + p.parts[-2] + '/'
remote_dir = remote_top_dir + p.parts[-3] + '/' + p.parts[-2] + '/'
log.info(' *** origin: %s' % fname_origin)
log.info(' *** destination: %s' % fname_destination)
# log.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.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.info(' *** Data transfer: Done!')
return 0
else:
log.error(' *** Quitting the copy operation')
return -1
def take_image(global_PVs, params):
log.info(' *** *** taking a single image')
nRow = global_PVs['Cam1SizeY_RBV'].get()
nCol = global_PVs['Cam1SizeX_RBV'].get()
image_size = nRow * nCol
global_PVs['Cam1NumImages'].put(1, wait=True)
global_PVs['Cam1TriggerMode'].put('Off', wait=True)
wait_time_sec = int(params.exposure_time) + 5
global_PVs['Cam1Acquire'].put(DetectorAcquire, wait=True, timeout=1000.0)
time.sleep(0.1)
if pv.wait_pv(global_PVs['Cam1Acquire'], DetectorIdle, wait_time_sec) == False: # adjust wait time
global_PVs['Cam1Acquire'].put(DetectorIdle)
# Get the image loaded in memory
img_vect = global_PVs['Cam1Image'].get(count=image_size)
img = np.reshape(img_vect,[nRow, nCol])
pixelFormat = global_PVs['Cam1PixelFormat_RBV'].get(as_string=True)
if (pixelFormat == "Mono16"):
pixel_f = 16
elif (pixelFormat == "Mono8"):
pixel_f = 8
else:
log.error(' *** *** bit %s format not supported' % pixelFormat)
exit()
img_uint = np.mod(img, 2**pixel_f)
return img_uint
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 tomo_fly_scan(global_PVs, params):
log.info(' ')
log.info(' *** start_scan')
def cleanup(signal, frame):
stop_scan(global_PVs, params)
sys.exit(0)
signal.signal(signal.SIGINT, cleanup)
# if params.has_key('StopTheScan'):
# stop_scan(global_PVs, params)
# return
# moved to outer loop in main()
# init(global_PVs, params)
set_image_factor(global_PVs, params)
rotation_start = params.sample_rotation_start
rotation_end = params.sample_rotation_end
if ((params.reverse == 'True') and ((params.scan_counter % 2) == 1)):
params.sample_rotation_start = rotation_end
params.sample_rotation_end = rotation_start
aps2bm.set_pso(global_PVs, params)
# fname = global_PVs['HDF1_FileName'].get(as_string=True)
log.info(' *** File name prefix: %s' % params.file_name)
flir.set(global_PVs, params)
aps2bm.open_shutters(global_PVs, params)
aps2bm.move_sample_in(global_PVs, params)
theta = flir.acquire(global_PVs, params)
if ((params.reverse == 'True') and ((params.scan_counter % 2) == 1)):
params.sample_rotation_start = rotation_start
params.sample_rotation_end = rotation_end
theta_end = global_PVs['Motor_SampleRot_RBV'].get()
if (0 < theta_end < 180.0):
# print('\x1b[2;30;41m' + ' *** Rotary Stage ERROR. Theta stopped at: ***' + theta_end + '\x1b[0m')
log.error(' *** Rotary Stage ERROR. Theta stopped at: %s ***' % str(theta_end))
aps2bm.move_sample_out(global_PVs, params)
flir.acquire_flat(global_PVs, params)
aps2bm.move_sample_in(global_PVs, params)
aps2bm.close_shutters(global_PVs, params)
time.sleep(2)
flir.acquire_dark(global_PVs, params)
flir.checkclose_hdf(global_PVs, params)
flir.add_theta(global_PVs, params, theta)
# update config file
config.update_config(params)
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 run(fname):
try:
# Form auto-complete for scan
out = subprocess.Popen(['tomo', 'scan', '-h'],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
stdout, _ = out.communicate()
stdout = str(stdout)
cmdscan = []
parscan = []
st = stdout.find("optional")
while (1):
st = stdout.find('--', st)
end = min(stdout.find(' ', st), stdout.find('\\n', st))
if (st < 0):
break
cmdscan.append(stdout[st:end])
st = stdout.find('(default:', end)
st1 = stdout.find('--', end)
if (st1 > st or st1 < 0):
end = stdout.find(')', st)
parscan.append(stdout[st + 9:end].replace(" ", "").replace(
"\\n", ""))
else:
parscan.append("")
st = end
# Create bash file
fid = open(fname, 'w')
fid.write(
'#/usr/bin/env bash\n _tomo()\n{\n\tlocal cur prev opts\n\tCOMPREPLY=()\n\tcur="${COMP_WORDS[COMP_CWORD]}"\n\tprev="${COMP_WORDS[COMP_CWORD-1]}"\n'
)
# check all tomo scan
fid.write('\tif [[ ${COMP_WORDS[1]} == "scan" ]] ; then\n')
fid.write('\t\topts="')
fid.write(' '.join(cmdscan))
fid.write('"\n')
fid.write(
'\t\tCOMPREPLY=( $(compgen -W "${opts}" -- ${cur}) )\n\tfi\n')
for k in range(len(cmdscan)):
fid.write('\tif [[ ${prev} == "')
fid.write(cmdscan[k])
fid.write('" ]] ; then\n')
fid.write('\t\topts="')
fid.write(parscan[k])
fid.write('"\n')
fid.write(
'\t\tCOMPREPLY=( $(compgen -W "${opts}" -- ${cur}) )\n\t\treturn 0\n\tfi\n'
)
fid.write('}\n')
fid.write('complete -F _tomo tomo')
fid.close()
except:
log.error('Autocomplete file was not created')
def _setup_hdf_writer(global_PVs, params, fname=None):
if (params.camera_ioc_prefix == '2bmbPG3:') or (params.camera_ioc_prefix
== '2bmbSP1:'):
# setup Point Grey hdf writer PV's
log.info(' ')
log.info(' *** setup hdf_writer')
_setup_frame_type(global_PVs, params)
if params.recursive_filter == True:
log.info(' *** Recursive Filter Enabled')
global_PVs['Proc1_Enable_Background'].put('Disable', wait=True)
global_PVs['Proc1_Enable_FlatField'].put('Disable', wait=True)
global_PVs['Proc1_Enable_Offset_Scale'].put('Disable', wait=True)
global_PVs['Proc1_Enable_Low_Clip'].put('Disable', wait=True)
global_PVs['Proc1_Enable_High_Clip'].put('Disable', wait=True)
global_PVs['Proc1_Callbacks'].put('Enable', wait=True)
global_PVs['Proc1_Filter_Enable'].put('Enable', wait=True)
global_PVs['HDF1_ArrayPort'].put('PROC1', wait=True)
global_PVs['Proc1_Filter_Type'].put(Recursive_Filter_Type,
wait=True)
global_PVs['Proc1_Num_Filter'].put(int(
params.recursive_filter_n_images),
wait=True)
global_PVs['Proc1_Reset_Filter'].put(1, wait=True)
global_PVs['Proc1_AutoReset_Filter'].put('Yes', wait=True)
global_PVs['Proc1_Filter_Callbacks'].put('Array N only', wait=True)
log.info(' *** Recursive Filter Enabled: Done!')
else:
global_PVs['Proc1_Filter_Enable'].put('Disable')
global_PVs['HDF1_ArrayPort'].put(
global_PVs['Proc1_ArrayPort'].get())
global_PVs['HDF1_AutoSave'].put('Yes')
global_PVs['HDF1_DeleteDriverFile'].put('No')
global_PVs['HDF1_EnableCallbacks'].put('Enable')
global_PVs['HDF1_BlockingCallbacks'].put('No')
# if (params.recursive_filter == False):
# params.recursive_filter_n_images = 1
totalProj = ((int(params.num_projections / params.recursive_filter_n_images)) + int(params.num_dark_images) + \
int(params.num_white_images))
global_PVs['HDF1_NumCapture'].put(totalProj)
global_PVs['HDF1_FileWriteMode'].put(str(params.file_write_mode),
wait=True)
if fname is not None:
global_PVs['HDF1_FileName'].put(str(fname), wait=True)
global_PVs['HDF1_Capture'].put(1)
aps2bm.wait_pv(global_PVs['HDF1_Capture'], 1)
log.info(' *** setup hdf_writer: Done!')
else:
log.error('Detector %s is not defined' % params.camera_ioc_prefix)
return
def create_remote_directory(remote_server, remote_dir):
cmd = 'mkdir -p ' + remote_dir
try:
# log.info(' *** sending command %s' % (cmd))
log.info(' *** creating remote directory %s' % (remote_dir))
subprocess.check_call(['ssh', remote_server, cmd])
log.info(' *** creating remote directory %s: Done!' % (remote_dir))
return 0
except subprocess.CalledProcessError as e:
log.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.warning(' *** remote directory %s exists' % (remote_dir))
return 0
except subprocess.CalledProcessError as e:
# log.info(' *** return code = %d' % (e.returncode))
log.warning(' *** remote directory %s does not exist' % (remote_dir))
if e.returncode == 2:
return e.returncode
else:
log.error(' *** Unknown error code returned: %d' % (e.returncode))
return -1
def dummy_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))
except KeyError:
log.error(' *** Some PV assignment failed!')
pass
def checkclose_hdf(global_PVs, params):
buffer_queue = global_PVs['HDFQueueSize'].get() - global_PVs['HDFQueueFree'].get()
# wait_on_hdd = 10
frate = 55.0
wait_on_hdd = buffer_queue / frate + 10
# wait_on_hdd = (global_PVs['HDFQueueSize'].get() - global_PVs['HDFQueueFree'].get()) / 55.0 + 10
log.info(' *** Buffer Queue (frames): %d ' % buffer_queue)
log.info(' *** Wait HDD (s): %f' % wait_on_hdd)
if pv.wait_pv(global_PVs["HDFCapture_RBV"], 0, wait_on_hdd) == False: # needs to wait for HDF plugin queue to dump to disk
global_PVs["HDFCapture"].put(0)
log.info(' *** File was not closed => forced to close')
log.info(' *** before %d' % global_PVs["HDFCapture_RBV"].get())
pv.wait_pv(global_PVs["HDFCapture_RBV"], 0, 5)
log.info(' *** after %d' % global_PVs["HDFCapture_RBV"].get())
if (global_PVs["HDFCapture_RBV"].get() == 1):
log.error(' *** ERROR HDF FILE DID NOT CLOSE; add_theta will fail')
def update_config(args):
# update tomo2bm.conf
sections = SCAN_PARAMS
write(args.config, args=args, sections=sections)
# copy tomo2bm.conf to the raw data directory with a unique name (sample_name.conf)
log_fname = args.file_path + os.sep + args.file_name + '.conf'
try:
shutil.copyfile(args.config, log_fname)
log.info(' *** copied %s to %s ' % (args.config, log_fname))
except:
log.error(' *** attempt to copy %s to %s failed' %
(args.config, log_fname))
pass
log.warning(
' *** command to repeat the scan: tomo scan --config {:s}'.format(
log_fname))
if (args.dx_update):
write_hdf(args, sections)
def set_pso(global_PVs, params):
acclTime = 1.0 * params.slew_speed / params.accl_rot
scanDelta = abs(((float(params.sample_rotation_end) -
float(params.sample_rotation_start))) /
((float(params.num_projections)) *
float(params.recursive_filter_n_images)))
log.info(' *** *** start_pos %f' % float(params.sample_rotation_start))
log.info(' *** *** end pos %f' % float(params.sample_rotation_end))
global_PVs['Fly_StartPos'].put(float(params.sample_rotation_start),
wait=True)
global_PVs['Fly_EndPos'].put(float(params.sample_rotation_end), wait=True)
global_PVs['Fly_SlewSpeed'].put(params.slew_speed, wait=True)
global_PVs['Fly_ScanDelta'].put(scanDelta, wait=True)
time.sleep(3.0)
calc_num_proj = global_PVs['Fly_Calc_Projections'].get()
if calc_num_proj == None:
log.error(
' *** *** Error getting fly calculated number of projections!')
calc_num_proj = global_PVs['Fly_Calc_Projections'].get()
log.error(' *** *** Using %s instead of %s' %
(calc_num_proj, params.num_projections))
if calc_num_proj != int(params.num_projections):
log.warning(
' *** *** Changing number of projections from: %s to: %s' %
(params.num_projections, int(calc_num_proj)))
params.num_projections = int(calc_num_proj)
log.info(' *** *** Number of projections: %d' %
int(params.num_projections))
log.info(' *** *** Fly calc triggers: %d' % int(calc_num_proj))
global_PVs['Fly_ScanControl'].put('Standard')
log.info(' ')
log.info(' *** Taxi before starting capture')
global_PVs['Fly_Taxi'].put(1, wait=True)
wait_pv(global_PVs['Fly_Taxi'], 0)
log.info(' *** Taxi before starting capture: Done!')
def init_general_PVs(global_PVs, params):
# shutter pv's
global_PVs['ShutterA_Open'] = PV('7bma:A_shutter:open.VAL')
global_PVs['ShutterA_Close'] = PV('7bma:A_shutter:close.VAL')
global_PVs['ShutterA_Move_Status'] = PV('PA:02BM:STA_A_FES_OPEN_PL')
# Experimment Info
global_PVs['Sample_Name'] = PV('2bmS1:ExpInfo:SampleName')
global_PVs['User_Badge'] = PV('2bmS1:ExpInfo:UserBadge.VAL')
global_PVs['User_Email'] = PV('2bmS1:ExpInfo:UserEmail.VAL')
global_PVs['User_Institution'] = PV('2bmS1:ExpInfo:UserInstitution.VAL')
global_PVs['Proposal_Number'] = PV('2bmS1:ExpInfo:ProposalNumber.VAL')
global_PVs['Proposal_Title'] = PV('2bmS1:ExpInfo:ProposalTitle.VAL')
global_PVs['Sample_Description'] = PV('2bmS1:ExpInfo:SampleDescription.VAL')
global_PVs['User_Info_Update'] = PV('2bmS1:ExpInfo:UserInfoUpdate.VAL')
global_PVs['Lens_Magnification'] = PV('2bmS1:ExpInfo:LensMagnification.VAL')
global_PVs['Scintillator_Type'] = PV('2bmS1:ExpInfo:ScintillatorType.VAL')
global_PVs['Filters'] = PV('2bmS1:ExpInfo:Filters.VAL')
global_PVs['File_Name'] = PV('2bmS1:ExpInfo:FileName.VAL')
global_PVs['Station'] = PV('2bmS1:ExpInfo:Station.VAL')
global_PVs['Camera_IOC_Prefix'] = PV('2bmS1:ExpInfo:CameraIOCPrefix.VAL')
global_PVs['Remote_Analysis_Dir'] = PV('2bmS1:ExpInfo:RemoteAnalysisDir.VAL')
global_PVs['User_Last_Name'] = PV('2bmS1:ExpInfo:UserLastName.VAL')
global_PVs['Experiment_Year_Month'] = PV('2bmS1:ExpInfo:ExperimentYearMonth.VAL')
global_PVs['Use_Furnace'] = PV('2bmS1:ExpInfo:UseFurnace.VAL')
global_PVs['White_Field_Motion'] = PV('2bmS1:ExpInfo:WhiteFieldMotion.VAL')
global_PVs['Remote_Data_Trasfer'] = PV('2bmS1:ExpInfo:RemoteDataTrasfer.VAL')
global_PVs['Scan_Type'] = PV('2bmS1:ExpInfo:ScanType.VAL')
global_PVs['Num_Projections'] = PV('2bmS1:ExpInfo:NumProjections.VAL')
global_PVs['Num_White_Images'] = PV('2bmS1:ExpInfo:NumWhiteImages.VAL')
global_PVs['Num_Dark_Images'] = PV('2bmS1:ExpInfo:NumDarkImages.VAL')
global_PVs['Scintillator_Thickness'] = PV('2bmS1:ExpInfo:ScintillatorThickness.VAL')
global_PVs['Sample_Detector_Distance'] = PV('2bmS1:ExpInfo:SampleDetectorDistance.VAL')
global_PVs['Sample_In_Position'] = PV('2bmS1:ExpInfo:SampleInPosition.VAL')
global_PVs['Sample_Out_Position'] = PV('2bmS1:ExpInfo:SampleOutPosition.VAL')
global_PVs['Sample_Rotation_Start'] = PV('2bmS1:ExpInfo:SampleRotationStart.VAL')
global_PVs['Sample_Rotation_End'] = PV('2bmS1:ExpInfo:SampleRotationEnd.VAL')
global_PVs['Furnace_In_Position'] = PV('2bmS1:ExpInfo:FurnaceInPosition.VAL')
global_PVs['Furnace_Out_Position'] = PV('2bmS1:ExpInfo:FurnaceOutPosition.VAL')
global_PVs['Sleep_Time'] = PV('2bmS1:ExpInfo:SleepTime.VAL')
global_PVs['Vertical_Scan_Start'] = PV('2bmS1:ExpInfo:VerticalScanStart.VAL')
global_PVs['Vertical_Scan_End'] = PV('2bmS1:ExpInfo:VerticalScanEnd.VAL')
global_PVs['Vertical_Scan_Step_Size'] = PV('2bmS1:ExpInfo:VerticalScanStepSize.VAL')
global_PVs['Horizontal_Scan_Start'] = PV('2bmS1:ExpInfo:HorizontalScanStart.VAL')
global_PVs['Horizontal_Scan_End'] = PV('2bmS1:ExpInfo:HorizontalScanEnd.VAL')
global_PVs['Horizontal_Scan_Step_Size'] = PV('2bmS1:ExpInfo:HorizontalScanStepSize.VAL')
if params.station == '2-BM-A':
log.info('*** Running in station A:')
# Set sample stack motor pv's:
global_PVs['Motor_SampleX'] = PV('2bma:m49.VAL')
global_PVs['Motor_SampleX_SET'] = PV('2bma:m49.SET')
global_PVs['Motor_SampleY'] = PV('2bma:m20.VAL')
global_PVs['Motor_SampleRot'] = PV('2bma:m82.VAL') # Aerotech ABR-250
global_PVs['Motor_SampleRot_RBV'] = PV('2bma:m82.RBV') # Aerotech ABR-250
global_PVs['Motor_SampleRot_Cnen'] = PV('2bma:m82.CNEN')
global_PVs['Motor_SampleRot_Accl'] = PV('2bma:m82.ACCL')
global_PVs['Motor_SampleRot_Stop'] = PV('2bma:m82.STOP')
global_PVs['Motor_SampleRot_Set'] = PV('2bma:m82.SET')
global_PVs['Motor_SampleRot_Velo'] = PV('2bma:m82.VELO')
global_PVs['Motor_Sample_Top_0'] = PV('2bmS1:m2.VAL')
global_PVs['Motor_Sample_Top_90'] = PV('2bmS1:m1.VAL')
# Set FlyScan
global_PVs['Fly_ScanDelta'] = PV('2bma:PSOFly2:scanDelta')
global_PVs['Fly_StartPos'] = PV('2bma:PSOFly2:startPos')
global_PVs['Fly_EndPos'] = PV('2bma:PSOFly2:endPos')
global_PVs['Fly_SlewSpeed'] = PV('2bma:PSOFly2:slewSpeed')
global_PVs['Fly_Taxi'] = PV('2bma:PSOFly2:taxi')
global_PVs['Fly_Run'] = PV('2bma:PSOFly2:fly')
global_PVs['Fly_ScanControl'] = PV('2bma:PSOFly2:scanControl')
global_PVs['Fly_Calc_Projections'] = PV('2bma:PSOFly2:numTriggers')
global_PVs['Theta_Array'] = PV('2bma:PSOFly2:motorPos.AVAL')
global_PVs['Fast_Shutter'] = PV('2bma:m23.VAL')
global_PVs['Motor_Focus'] = PV('2bma:m41.VAL')
global_PVs['Motor_Focus_Name'] = PV('2bma:m41.DESC')
elif params.station == '2-BM-B':
log.info('*** Running in station B:')
# Sample stack motor pv's:
global_PVs['Motor_SampleX'] = PV('2bmb:m63.VAL')
global_PVs['Motor_SampleX_SET'] = PV('2bmb:m63.SET')
global_PVs['Motor_SampleY'] = PV('2bmb:m57.VAL')
global_PVs['Motor_SampleRot'] = PV('2bmb:m100.VAL') # Aerotech ABR-150
global_PVs['Motor_SampleRot_Accl'] = PV('2bma:m100.ACCL')
global_PVs['Motor_SampleRot_Stop'] = PV('2bma:m100.STOP')
global_PVs['Motor_SampleRot_Set'] = PV('2bma:m100.SET')
global_PVs['Motor_SampleRot_Velo'] = PV('2bma:m100.VELO')
global_PVs['Motor_Sample_Top_0'] = PV('2bmb:m76.VAL')
global_PVs['Motor_Sample_Top_90'] = PV('2bmb:m77.VAL')
# Set CCD stack motor PVs:
global_PVs['Motor_CCD_Z'] = PV('2bmb:m31.VAL')
# Set FlyScan
global_PVs['Fly_ScanDelta'] = PV('2bmb:PSOFly:scanDelta')
global_PVs['Fly_StartPos'] = PV('2bmb:PSOFly:startPos')
global_PVs['Fly_EndPos'] = PV('2bmb:PSOFly:endPos')
global_PVs['Fly_SlewSpeed'] = PV('2bmb:PSOFly:slewSpeed')
global_PVs['Fly_Taxi'] = PV('2bmb:PSOFly:taxi')
global_PVs['Fly_Run'] = PV('2bmb:PSOFly:fly')
global_PVs['Fly_ScanControl'] = PV('2bmb:PSOFly:scanControl')
global_PVs['Fly_Calc_Projections'] = PV('2bmb:PSOFly:numTriggers')
global_PVs['Theta_Array'] = PV('2bmb:PSOFly:motorPos.AVAL')
global_PVs['Motor_Focus'] = PV('2bmb:m78.VAL')
global_PVs['Motor_Focus_Name'] = PV('2bmb:m78.DESC')
else:
log.error('*** %s is not a valid station' % params.station)
# detector pv's
if ((params.camera_ioc_prefix == '2bmbPG3:') or (params.camera_ioc_prefix == '2bmbSP1:')):
# init Point Grey PV's
# general PV's
global_PVs['Cam1_SerialNumber'] = PV(params.camera_ioc_prefix + 'cam1:SerialNumber_RBV')
global_PVs['Cam1_ImageMode'] = PV(params.camera_ioc_prefix + 'cam1:ImageMode')
global_PVs['Cam1_ArrayCallbacks'] = PV(params.camera_ioc_prefix + 'cam1:ArrayCallbacks')
global_PVs['Cam1_AcquirePeriod'] = PV(params.camera_ioc_prefix + 'cam1:AcquirePeriod')
global_PVs['Cam1_TriggerMode'] = PV(params.camera_ioc_prefix + 'cam1:TriggerMode')
global_PVs['Cam1_SoftwareTrigger'] = PV(params.camera_ioc_prefix + 'cam1:SoftwareTrigger') ### ask Mark is this is exposed in the medm screen
global_PVs['Cam1_AcquireTime'] = PV(params.camera_ioc_prefix + 'cam1:AcquireTime')
global_PVs['Cam1_FrameType'] = PV(params.camera_ioc_prefix + 'cam1:FrameType')
global_PVs['Cam1_NumImages'] = PV(params.camera_ioc_prefix + 'cam1:NumImages')
global_PVs['Cam1_Acquire'] = PV(params.camera_ioc_prefix + 'cam1:Acquire')
global_PVs['Cam1_AttributeFile'] = PV(params.camera_ioc_prefix + 'cam1:NDAttributesFile')
global_PVs['Cam1_FrameTypeZRST'] = PV(params.camera_ioc_prefix + 'cam1:FrameType.ZRST')
global_PVs['Cam1_FrameTypeONST'] = PV(params.camera_ioc_prefix + 'cam1:FrameType.ONST')
global_PVs['Cam1_FrameTypeTWST'] = PV(params.camera_ioc_prefix + 'cam1:FrameType.TWST')
global_PVs['Cam1_Display'] = PV(params.camera_ioc_prefix + 'image1:EnableCallbacks')
global_PVs['Cam1_SizeX'] = PV(params.camera_ioc_prefix + 'cam1:SizeX')
global_PVs['Cam1_SizeY'] = PV(params.camera_ioc_prefix + 'cam1:SizeY')
global_PVs['Cam1_SizeX_RBV'] = PV(params.camera_ioc_prefix + 'cam1:SizeX_RBV')
global_PVs['Cam1_SizeY_RBV'] = PV(params.camera_ioc_prefix + 'cam1:SizeY_RBV')
global_PVs['Cam1_MaxSizeX_RBV'] = PV(params.camera_ioc_prefix + 'cam1:MaxSizeX_RBV')
global_PVs['Cam1_MaxSizeY_RBV'] = PV(params.camera_ioc_prefix + 'cam1:MaxSizeY_RBV')
global_PVs['Cam1PixelFormat_RBV'] = PV(params.camera_ioc_prefix + 'cam1:PixelFormat_RBV')
global_PVs['Cam1_Image'] = PV(params.camera_ioc_prefix + 'image1:ArrayData')
# hdf5 writer PV's
global_PVs['HDF1_AutoSave'] = PV(params.camera_ioc_prefix + 'HDF1:AutoSave')
global_PVs['HDF1_DeleteDriverFile'] = PV(params.camera_ioc_prefix + 'HDF1:DeleteDriverFile')
global_PVs['HDF1_EnableCallbacks'] = PV(params.camera_ioc_prefix + 'HDF1:EnableCallbacks')
global_PVs['HDF1_BlockingCallbacks'] = PV(params.camera_ioc_prefix + 'HDF1:BlockingCallbacks')
global_PVs['HDF1_FileWriteMode'] = PV(params.camera_ioc_prefix + 'HDF1:FileWriteMode')
global_PVs['HDF1_NumCapture'] = PV(params.camera_ioc_prefix + 'HDF1:NumCapture')
global_PVs['HDF1_Capture'] = PV(params.camera_ioc_prefix + 'HDF1:Capture')
global_PVs['HDF1_Capture_RBV'] = PV(params.camera_ioc_prefix + 'HDF1:Capture_RBV')
global_PVs['HDF1_FilePath'] = PV(params.camera_ioc_prefix + 'HDF1:FilePath')
global_PVs['HDF1_FileName'] = PV(params.camera_ioc_prefix + 'HDF1:FileName')
global_PVs['HDF1_FullFileName_RBV'] = PV(params.camera_ioc_prefix + 'HDF1:FullFileName_RBV')
global_PVs['HDF1_FileTemplate'] = PV(params.camera_ioc_prefix + 'HDF1:FileTemplate')
global_PVs['HDF1_ArrayPort'] = PV(params.camera_ioc_prefix + 'HDF1:NDArrayPort')
global_PVs['HDF1_FileNumber'] = PV(params.camera_ioc_prefix + 'HDF1:FileNumber')
global_PVs['HDF1_XMLFileName'] = PV(params.camera_ioc_prefix + 'HDF1:XMLFileName')
global_PVs['HDF1_QueueSize'] = PV(params.camera_ioc_prefix + 'HDF1:QueueSize')
global_PVs['HDF1_QueueFree'] = PV(params.camera_ioc_prefix + 'HDF1:QueueFree')
# proc1 PV's
global_PVs['Image1_Callbacks'] = PV(params.camera_ioc_prefix + 'image1:EnableCallbacks')
global_PVs['Proc1_Callbacks'] = PV(params.camera_ioc_prefix + 'Proc1:EnableCallbacks')
global_PVs['Proc1_ArrayPort'] = PV(params.camera_ioc_prefix + 'Proc1:NDArrayPort')
global_PVs['Proc1_Filter_Enable'] = PV(params.camera_ioc_prefix + 'Proc1:EnableFilter')
global_PVs['Proc1_Filter_Type'] = PV(params.camera_ioc_prefix + 'Proc1:FilterType')
global_PVs['Proc1_Num_Filter'] = PV(params.camera_ioc_prefix + 'Proc1:NumFilter')
global_PVs['Proc1_Reset_Filter'] = PV(params.camera_ioc_prefix + 'Proc1:ResetFilter')
global_PVs['Proc1_AutoReset_Filter'] = PV(params.camera_ioc_prefix + 'Proc1:AutoResetFilter')
global_PVs['Proc1_Filter_Callbacks'] = PV(params.camera_ioc_prefix + 'Proc1:FilterCallbacks')
global_PVs['Proc1_Enable_Background'] = PV(params.camera_ioc_prefix + 'Proc1:EnableBackground')
global_PVs['Proc1_Enable_FlatField'] = PV(params.camera_ioc_prefix + 'Proc1:EnableFlatField')
global_PVs['Proc1_Enable_Offset_Scale'] = PV(params.camera_ioc_prefix + 'Proc1:EnableOffsetScale')
global_PVs['Proc1_Enable_Low_Clip'] = PV(params.camera_ioc_prefix + 'Proc1:EnableLowClip')
global_PVs['Proc1_Enable_High_Clip'] = PV(params.camera_ioc_prefix + 'Proc1:EnableHighClip')
if (params.camera_ioc_prefix == '2bmbPG3:'):
global_PVs['Cam1_FrameRateOnOff'] = PV(params.camera_ioc_prefix + 'cam1:FrameRateOnOff')
elif (params.camera_ioc_prefix == '2bmbSP1:'):
global_PVs['Cam1_AcquireTimeAuto'] = PV(params.camera_ioc_prefix + 'cam1:AcquireTimeAuto')
global_PVs['Cam1_FrameRateOnOff'] = PV(params.camera_ioc_prefix + 'cam1:FrameRateEnable')
global_PVs['Cam1_TriggerSource'] = PV(params.camera_ioc_prefix + 'cam1:TriggerSource')
global_PVs['Cam1_TriggerOverlap'] = PV(params.camera_ioc_prefix + 'cam1:TriggerOverlap')
global_PVs['Cam1_ExposureMode'] = PV(params.camera_ioc_prefix + 'cam1:ExposureMode')
global_PVs['Cam1_TriggerSelector'] = PV(params.camera_ioc_prefix + 'cam1:TriggerSelector')
global_PVs['Cam1_TriggerActivation'] = PV(params.camera_ioc_prefix + 'cam1:TriggerActivation')
else:
log.error('Detector %s is not defined' % params.camera_ioc_prefix)
return
user_info_update(global_PVs, params)
return global_PVs
def set(global_PVs, params):
fname = params.file_name
# Set detectors
if (params.camera_ioc_prefix == '2bmbPG3:'):
log.info(' ')
log.info(' *** setup Point Grey')
# mona runf always in B with PG camera
global_PVs['Cam1AttributeFile'].put('monaDetectorAttributes.xml', wait=True)
global_PVs['HDFXMLFileName'].put('monaLayout.xml', wait=True)
global_PVs['Cam1ImageMode'].put('Multiple')
global_PVs['Cam1ArrayCallbacks'].put('Enable')
#global_PVs['Image1_Callbacks'].put('Enable')
global_PVs['Cam1AcquirePeriod'].put(float(params.exposure_time))
global_PVs['Cam1AcquireTime'].put(float(params.exposure_time))
# if we are using external shutter then set the exposure time
global_PVs['Cam1FrameRateOnOff'].put(0)
wait_time_sec = int(params.exposure_time) + 5
global_PVs['Cam1TriggerMode'].put('Overlapped', wait=True) #Ext. Standard
global_PVs['Cam1NumImages'].put(1, wait=True)
global_PVs['Cam1Acquire'].put(DetectorAcquire)
pv.wait_pv(global_PVs['Cam1Acquire'], DetectorAcquire, 2)
global_PVs['Cam1SoftwareTrigger'].put(1)
pv.wait_pv(global_PVs['Cam1Acquire'], DetectorIdle, wait_time_sec)
global_PVs['Cam1Acquire'].put(DetectorAcquire)
pv.wait_pv(global_PVs['Cam1Acquire'], DetectorAcquire, 2)
global_PVs['Cam1SoftwareTrigger'].put(1)
pv.wait_pv(global_PVs['Cam1Acquire'], DetectorIdle, wait_time_sec)
log.info(' *** setup Point Grey: Done!')
elif (params.camera_ioc_prefix == '2bmbSP1:'):
log.info(' ')
log.info(' *** setup FLIR camera')
if params.station == '2-BM-A':
global_PVs['Cam1AttributeFile'].put('flir2bmaDetectorAttributes.xml')
global_PVs['HDFXMLFileName'].put('flir2bmaLayout.xml')
else: # Mona (B-station)
global_PVs['Cam1AttributeFile'].put('flir2bmbDetectorAttributes.xml', wait=True)
global_PVs['HDFXMLFileName'].put('flir2bmbLayout.xml', wait=True)
global_PVs['Cam1Acquire'].put(DetectorIdle)
pv.wait_pv(global_PVs['Cam1Acquire'], DetectorIdle, 2)
global_PVs['Cam1TriggerMode'].put('Off', wait=True)
global_PVs['Cam1TriggerSource'].put('Line2', wait=True)
global_PVs['Cam1TriggerOverlap'].put('ReadOut', wait=True)
global_PVs['Cam1ExposureMode'].put('Timed', wait=True)
global_PVs['Cam1TriggerSelector'].put('FrameStart', wait=True)
global_PVs['Cam1TriggerActivation'].put('RisingEdge', wait=True)
global_PVs['Cam1ImageMode'].put('Multiple')
global_PVs['Cam1ArrayCallbacks'].put('Enable')
#global_PVs['Image1_Callbacks'].put('Enable')
#global_PVs['Cam1AcquirePeriod'].put(float(params.exposure_time))
global_PVs['Cam1FrameRateOnOff'].put(0)
global_PVs['Cam1AcquireTimeAuto'].put('Off')
global_PVs['Cam1AcquireTime'].put(float(params.exposure_time))
# if we are using external shutter then set the exposure time
wait_time_sec = int(params.exposure_time) + 5
global_PVs['Cam1TriggerMode'].put('On', wait=True)
log.info(' *** setup FLIR camera: Done!')
else:
log.error('Detector %s is not defined' % params.camera_ioc_prefix)
return
if fname is None:
log.warning(' *** hdf_writer will not be configured')
else:
_setup_hdf_writer(global_PVs, params, fname)
def init_general_PVs(params):
global_PVs = {}
global_PVs['Station'] = PV('2bmS1:ExpInfo:Station.VAL')
global_PVs['Camera_IOC_Prefix'] = PV('2bmS1:ExpInfo:CameraIOCPrefix.VAL')
# shutter pv's
global_PVs['ShutterAOpen'] = PV('2bma:A_shutter:open.VAL')
global_PVs['ShutterAClose'] = PV('2bma:A_shutter:close.VAL')
global_PVs['ShutterAMoveStatus'] = PV('PA:02BM:STA_A_FES_OPEN_PL')
global_PVs['ShutterBOpen'] = PV('2bma:B_shutter:open.VAL')
global_PVs['ShutterB_Close'] = PV('2bma:B_shutter:close.VAL')
global_PVs['ShutterB_Move_Status'] = PV('PA:02BM:STA_B_SBS_OPEN_PL')
# Experimment Info
global_PVs['UserName'] = PV('2bmS1:ExpInfo:UserName.VAL')
global_PVs['UserEmail'] = PV('2bmS1:ExpInfo:UserEmail.VAL')
global_PVs['UserBadge'] = PV('2bmS1:ExpInfo:UserBadge.VAL')
global_PVs['ProposalNumber'] = PV('2bmS1:ExpInfo:ProposalNumber.VAL')
global_PVs['ProposalTitle'] = PV('2bmS1:ExpInfo:ProposalTitle.VAL')
global_PVs['UserInstitution'] = PV('2bmS1:ExpInfo:UserInstitution.VAL')
global_PVs['UserInfoUpdate'] = PV('2bmS1:ExpInfo:UserInfoUpdate.VAL')
global_PVs['Time'] = PV('S:IOC:timeOfDayISO8601')
global_PVs['ScintillatorType'] = PV('2bmS1:ExpInfo:ScintillatorType.VAL')
global_PVs['ScintillatorThickness'] = PV(
'2bmS1:ExpInfo:ScintillatorThickness.VAL')
global_PVs['ImagePixelSize'] = PV('2bmS1:ExpInfo:ImagePixelSize.VAL')
global_PVs['DetectorPixelSize'] = PV('2bmS1:ExpInfo:DetectorPixelSize.VAL')
global_PVs['CameraObjective'] = PV('2bmS1:CameraObjective.VAL')
global_PVs['CameraTubeLength'] = PV('22bmS1:ExpInfo:CameraTubeLength.VAL')
# energy info
global_PVs['Energy'] = PV('2bmS1:ExpInfo:Energy.VAL')
global_PVs['EnergyMode'] = PV('2bmS1:ExpInfo:EnergyMode.VAL')
global_PVs['Filters'] = PV('2bmS1:ExpInfo:Filters.VAL')
# scan info
global_PVs['RotationStart'] = PV('2bmS1:ExpInfo:RotationStart.VAL')
global_PVs['RotationEnd'] = PV('2bmS1:ExpInfo:RotationEnd.VAL')
global_PVs['RotationStep'] = PV('2bmS1:ExpInfo:RotationStep.VAL')
global_PVs['NumAngles'] = PV('2bmS1:ExpInfo:NumAngles.VAL')
global_PVs['ReturnRotation'] = PV('2bmS1:ExpInfo:ReturnRotation')
global_PVs['NumFlatFields'] = PV('2bmS1:ExpInfo:NumFlatFields.VAL')
global_PVs['FlatFieldMode'] = PV('2bmS1:ExpInfo:FlatFieldMode')
global_PVs['FlatFieldValue'] = PV('2bmS1:ExpInfo:FlatFieldValue')
global_PVs['NumDarkFields'] = PV('2bmS1:ExpInfo:NumDarkFields.VAL')
global_PVs['DarkFieldMode'] = PV('2bmS1:ExpInfo:DarkFieldMode')
global_PVs['DarkFieldValue'] = PV('2bmS1:ExpInfo:DarkFieldValue')
global_PVs['FlatFieldAxis'] = PV('2bmS1:ExpInfo:FlatFieldAxis')
global_PVs['SampleInX'] = PV('2bmS1:ExpInfo:SampleInX')
global_PVs['SampleOutX'] = PV('2bmS1:ExpInfo:SampleOutX')
global_PVs['SampleInY'] = PV('2bmS1:ExpInfo:SampleInY')
global_PVs['SampleOutY'] = PV('2bmS1:ExpInfo:SampleOutY')
global_PVs['ScanType'] = PV('2bmS1:ExpInfo:ScanType.VAL')
global_PVs['SleepTime'] = PV('2bmS1:ExpInfo:SleepTime.VAL')
global_PVs['VerticalScanStart'] = PV('2bmS1:ExpInfo:VerticalScanStart.VAL')
global_PVs['VerticalScanEnd'] = PV('2bmS1:ExpInfo:VerticalScanEnd.VAL')
global_PVs['VerticalScanStepSize'] = PV(
'2bmS1:ExpInfo:VerticalScanStepSize.VAL')
global_PVs['HorizontalScanStart'] = PV(
'2bmS1:ExpInfo:HorizontalScanStart.VAL')
global_PVs['HorizontalScanEnd'] = PV('2bmS1:ExpInfo:HorizontalScanEnd.VAL')
global_PVs['HorizontalScanStepSize'] = PV(
'2bmS1:ExpInfo:HorizontalScanStepSize.VAL')
# sample info
global_PVs['SampleName'] = PV('2bmS1:ExpInfo:SampleName')
global_PVs['SampleDescription1'] = PV(
'2bmS1:ExpInfo:SampleDescription1.VAL')
global_PVs['SampleDescription2'] = PV(
'2bmS1:ExpInfo:SampleDescription2.VAL')
global_PVs['SampleDescription3'] = PV(
'2bmS1:ExpInfo:SampleDescription3.VAL')
# environment info
global_PVs['UseFurnace'] = PV('2bmS1:ExpInfo:UseFurnace.VAL')
global_PVs['FurnaceInPosition'] = PV('2bmS1:ExpInfo:FurnaceInPosition.VAL')
global_PVs['FurnaceOutPosition'] = PV(
'2bmS1:ExpInfo:FurnaceOutPosition.VAL')
# data management info
global_PVs['ExperimentYearMonth'] = PV(
'2bmS1:ExpInfo:ExperimentYearMonth.VAL')
global_PVs['UserLastName'] = PV('2bmS1:ExpInfo:UserLastName.VAL')
global_PVs['RemoteDataTransfer'] = PV(
'2bmS1:ExpInfo:RemoteDataTrasfer.VAL')
global_PVs['RemoteAnalysisDir'] = PV('2bmS1:ExpInfo:RemoteAnalysisDir.VAL')
if params.station == '2-BM-A':
log.info('*** Running in station A:')
# Set sample stack motor pv's:
global_PVs['SampleX'] = PV('2bma:m49.VAL')
global_PVs['SampleXSET'] = PV('2bma:m49.SET')
global_PVs['SampleY'] = PV('2bma:m20.VAL')
global_PVs['SampleOmega'] = PV('2bma:m82.VAL') # Aerotech ABR-250
global_PVs['SampleOmegaRBV'] = PV('2bma:m82.RBV') # Aerotech ABR-250
global_PVs['SampleOmegaCnen'] = PV('2bma:m82.CNEN')
global_PVs['SampleOmegaAccl'] = PV('2bma:m82.ACCL')
global_PVs['SampleOmegaStop'] = PV('2bma:m82.STOP')
global_PVs['SampleOmegaSet'] = PV('2bma:m82.SET')
global_PVs['SampleOmegaVelo'] = PV('2bma:m82.VELO')
global_PVs['SampleXCent'] = PV('2bmS1:m2.VAL')
global_PVs['SampleZCent'] = PV('2bmS1:m1.VAL')
global_PVs['SamplePitch'] = PV('2bma:m50.VAL')
global_PVs['SampleRoll'] = PV('2bma:m51.VAL')
global_PVs['CameraDistance'] = PV('2bma:m22.VAL')
# Set FlyScan
global_PVs['FlyScanDelta'] = PV('2bma:PSOFly2:scanDelta')
global_PVs['FlyStartPos'] = PV('2bma:PSOFly2:startPos')
global_PVs['FlyEndPos'] = PV('2bma:PSOFly2:endPos')
global_PVs['FlySlewSpeed'] = PV('2bma:PSOFly2:slewSpeed')
global_PVs['FlyTaxi'] = PV('2bma:PSOFly2:taxi')
global_PVs['FlyRun'] = PV('2bma:PSOFly2:fly')
global_PVs['FlyScanControl'] = PV('2bma:PSOFly2:scanControl')
global_PVs['FlyCalcProjections'] = PV('2bma:PSOFly2:numTriggers')
global_PVs['OmegaArray'] = PV('2bma:PSOFly2:motorPos.AVAL')
global_PVs['FastShutter'] = PV('2bma:m23.VAL')
global_PVs['Focus'] = PV('2bma:m41.VAL')
global_PVs['FocusName'] = PV('2bma:m41.DESC')
elif params.station == '2-BM-B':
log.info('*** Running in station B:')
# Sample stack motor pv's:
global_PVs['SampleX'] = PV('2bmb:m63.VAL')
global_PVs['SampleXSET'] = PV('2bmb:m63.SET')
global_PVs['SampleY'] = PV('2bmb:m57.VAL')
global_PVs['SampleOmega'] = PV('2bmb:m100.VAL') # Aerotech ABR-150
global_PVs['SampleOmegaAccl'] = PV('2bma:m100.ACCL')
global_PVs['SampleOmegaStop'] = PV('2bma:m100.STOP')
global_PVs['SampleOmegaSet'] = PV('2bma:m100.SET')
global_PVs['SampleOmegaVelo'] = PV('2bma:m100.VELO')
global_PVs['SampleXCent'] = PV('2bmb:m76.VAL')
global_PVs['SampleZCent'] = PV('2bmb:m77.VAL')
# Set CCD stack motor PVs:
global_PVs['Motor_CCD_Z'] = PV('2bmb:m31.VAL')
# Set FlyScan
global_PVs['FlyScanDelta'] = PV('2bmb:PSOFly:scanDelta')
global_PVs['FlyStartPos'] = PV('2bmb:PSOFly:startPos')
global_PVs['FlyEndPos'] = PV('2bmb:PSOFly:endPos')
global_PVs['FlySlewSpeed'] = PV('2bmb:PSOFly:slewSpeed')
global_PVs['FlyTaxi'] = PV('2bmb:PSOFly:taxi')
global_PVs['FlyRun'] = PV('2bmb:PSOFly:fly')
global_PVs['FlyScanControl'] = PV('2bmb:PSOFly:scanControl')
global_PVs['FlyCalcProjections'] = PV('2bmb:PSOFly:numTriggers')
global_PVs['OmegaArray'] = PV('2bmb:PSOFly:motorPos.AVAL')
global_PVs['Focus'] = PV('2bmb:m78.VAL')
global_PVs['FocusName'] = PV('2bmb:m78.DESC')
else:
log.error('*** %s is not a valid station' % params.station)
# detector pv's
if ((params.camera_ioc_prefix == '2bmbPG3:')
or (params.camera_ioc_prefix == '2bmbSP1:')):
# general PV's
global_PVs['Cam1SerialNumber'] = PV(params.camera_ioc_prefix +
'cam1:SerialNumber_RBV')
global_PVs['Cam1ImageMode'] = PV(params.camera_ioc_prefix +
'cam1:ImageMode')
global_PVs['Cam1ArrayCallbacks'] = PV(params.camera_ioc_prefix +
'cam1:ArrayCallbacks')
global_PVs['Cam1AcquirePeriod'] = PV(params.camera_ioc_prefix +
'cam1:AcquirePeriod')
global_PVs['Cam1TriggerMode'] = PV(params.camera_ioc_prefix +
'cam1:TriggerMode')
global_PVs['Cam1SoftwareTrigger'] = PV(
params.camera_ioc_prefix + 'cam1:SoftwareTrigger'
) ### ask Mark is this is exposed in the medm screen
global_PVs['Cam1AcquireTime'] = PV(params.camera_ioc_prefix +
'cam1:AcquireTime')
global_PVs['Cam1FrameType'] = PV(params.camera_ioc_prefix +
'cam1:FrameType')
global_PVs['Cam1NumImages'] = PV(params.camera_ioc_prefix +
'cam1:NumImages')
global_PVs['Cam1Acquire'] = PV(params.camera_ioc_prefix +
'cam1:Acquire')
global_PVs['Cam1AttributeFile'] = PV(params.camera_ioc_prefix +
'cam1:NDAttributesFile')
global_PVs['Cam1FrameTypeZRST'] = PV(params.camera_ioc_prefix +
'cam1:FrameType.ZRST')
global_PVs['Cam1FrameTypeONST'] = PV(params.camera_ioc_prefix +
'cam1:FrameType.ONST')
global_PVs['Cam1FrameTypeTWST'] = PV(params.camera_ioc_prefix +
'cam1:FrameType.TWST')
global_PVs['Cam1Display'] = PV(params.camera_ioc_prefix +
'image1:EnableCallbacks')
global_PVs['Cam1SizeX'] = PV(params.camera_ioc_prefix + 'cam1:SizeX')
global_PVs['Cam1SizeY'] = PV(params.camera_ioc_prefix + 'cam1:SizeY')
global_PVs['Cam1SizeX_RBV'] = PV(params.camera_ioc_prefix +
'cam1:SizeX_RBV')
global_PVs['Cam1SizeY_RBV'] = PV(params.camera_ioc_prefix +
'cam1:SizeY_RBV')
global_PVs['Cam1MaxSizeX_RBV'] = PV(params.camera_ioc_prefix +
'cam1:MaxSizeX_RBV')
global_PVs['Cam1MaxSizeY_RBV'] = PV(params.camera_ioc_prefix +
'cam1:MaxSizeY_RBV')
global_PVs['Cam1PixelFormat_RBV'] = PV(params.camera_ioc_prefix +
'cam1:PixelFormat_RBV')
global_PVs['Cam1Image'] = PV(params.camera_ioc_prefix +
'image1:ArrayData')
# hdf5 writer PV's
global_PVs['HDFAutoSave'] = PV(params.camera_ioc_prefix +
'HDF1:AutoSave')
global_PVs['HDFDeleteDriverFile'] = PV(params.camera_ioc_prefix +
'HDF1:DeleteDriverFile')
global_PVs['HDFEnableCallbacks'] = PV(params.camera_ioc_prefix +
'HDF1:EnableCallbacks')
global_PVs['HDFBlockingCallbacks'] = PV(params.camera_ioc_prefix +
'HDF1:BlockingCallbacks')
global_PVs['HDFFileWriteMode'] = PV(params.camera_ioc_prefix +
'HDF1:FileWriteMode')
global_PVs['HDFNumCapture'] = PV(params.camera_ioc_prefix +
'HDF1:NumCapture')
global_PVs['HDFCapture'] = PV(params.camera_ioc_prefix +
'HDF1:Capture')
global_PVs['HDFCapture_RBV'] = PV(params.camera_ioc_prefix +
'HDF1:Capture_RBV')
global_PVs['HDFFilePath'] = PV(params.camera_ioc_prefix +
'HDF1:FilePath')
global_PVs['HDFFileName'] = PV(params.camera_ioc_prefix +
'HDF1:FileName')
global_PVs['HDFFullFileName_RBV'] = PV(params.camera_ioc_prefix +
'HDF1:FullFileName_RBV')
global_PVs['HDFFileTemplate'] = PV(params.camera_ioc_prefix +
'HDF1:FileTemplate')
global_PVs['HDFArrayPort'] = PV(params.camera_ioc_prefix +
'HDF1:NDArrayPort')
global_PVs['HDFFileNumber'] = PV(params.camera_ioc_prefix +
'HDF1:FileNumber')
global_PVs['HDFXMLFileName'] = PV(params.camera_ioc_prefix +
'HDF1:XMLFileName')
global_PVs['HDFQueueSize'] = PV(params.camera_ioc_prefix +
'HDF1:QueueSize')
global_PVs['HDFQueueFree'] = PV(params.camera_ioc_prefix +
'HDF1:QueueFree')
# proc1 PV's
global_PVs['Image1EnableCallbacks'] = PV(params.camera_ioc_prefix +
'image1:EnableCallbacks')
global_PVs['Proc1nableCallbacks'] = PV(params.camera_ioc_prefix +
'Proc1:EnableCallbacks')
global_PVs['Proc1NDArrayPort'] = PV(params.camera_ioc_prefix +
'Proc1:NDArrayPort')
global_PVs['Proc1EnableFilter'] = PV(params.camera_ioc_prefix +
'Proc1:EnableFilter')
global_PVs['Proc1FilterType'] = PV(params.camera_ioc_prefix +
'Proc1:FilterType')
global_PVs['Proc1Num_Filter'] = PV(params.camera_ioc_prefix +
'Proc1:NumFilter')
global_PVs['Proc1ResetFilter'] = PV(params.camera_ioc_prefix +
'Proc1:ResetFilter')
global_PVs['Proc1AutoResetFilter'] = PV(params.camera_ioc_prefix +
'Proc1:AutoResetFilter')
global_PVs['Proc1FilterCallbacks'] = PV(params.camera_ioc_prefix +
'Proc1:FilterCallbacks')
global_PVs['Proc1EnableBackground'] = PV(params.camera_ioc_prefix +
'Proc1:EnableBackground')
global_PVs['Proc1EnableFlatField'] = PV(params.camera_ioc_prefix +
'Proc1:EnableFlatField')
global_PVs['Proc1EnableOffsetScale'] = PV(params.camera_ioc_prefix +
'Proc1:EnableOffsetScale')
global_PVs['Proc1EnableLowClip'] = PV(params.camera_ioc_prefix +
'Proc1:EnableLowClip')
global_PVs['Proc1EnableHighClip'] = PV(params.camera_ioc_prefix +
'Proc1:EnableHighClip')
if (params.camera_ioc_prefix == '2bmbPG3:'):
global_PVs['Cam1FrameRateOnOff'] = PV(params.camera_ioc_prefix +
'cam1:FrameRateOnOff')
elif (params.camera_ioc_prefix == '2bmbSP1:'):
global_PVs['Cam1AcquireTimeAuto'] = PV(params.camera_ioc_prefix +
'cam1:AcquireTimeAuto')
global_PVs['Cam1FrameRateOnOff'] = PV(params.camera_ioc_prefix +
'cam1:FrameRateEnable')
global_PVs['Cam1TriggerSource'] = PV(params.camera_ioc_prefix +
'cam1:TriggerSource')
global_PVs['Cam1TriggerOverlap'] = PV(params.camera_ioc_prefix +
'cam1:TriggerOverlap')
global_PVs['Cam1ExposureMode'] = PV(params.camera_ioc_prefix +
'cam1:ExposureMode')
global_PVs['Cam1TriggerSelector'] = PV(params.camera_ioc_prefix +
'cam1:TriggerSelector')
global_PVs['Cam1TriggerActivation'] = PV(params.camera_ioc_prefix +
'cam1:TriggerActivation')
else:
log.error('Detector %s is not defined' % params.camera_ioc_prefix)
return None
return global_PVs
def move_sample_in(global_PVs, params):
log.info(' *** Sample in')
if not (params.sample_move_freeze):
if (params.flat_field_axis == "vertical"):
log.info(' *** *** Move Sample Y in at: %f' %
params.sample_in_y)
global_PVs['SampleY'].put(str(params.sample_in_y),
wait=True,
timeout=1000.0)
if wait_pv(global_PVs['SampleY'], float(params.sample_in_y),
60) == False:
log.error('SampleY did not move in properly')
log.error(global_PVs['SampleY'].get())
else:
log.info(' *** *** Move Sample X in at: %f' %
params.sample_in_x)
global_PVs['SampleX'].put(str(params.sample_in_x),
wait=True,
timeout=1000.0)
if wait_pv(global_PVs['SampleX'], float(params.sample_in_x),
60) == False:
log.error('SampleX did not move in properly')
log.error(global_PVs['SampleX'].get())
if (params.use_furnace):
log.info(' *** *** Move Furnace Y in at: %f' %
params.furnace_in_position)
global_PVs['Motor_FurnaceY'].put(str(
params.furnace_in_position),
wait=True,
timeout=1000.0)
if wait_pv(global_PVs['Motor_FurnaceY'],
float(params.furnace_in_position), 60) == False:
log.error('Motor_FurnaceY did not move in properly')
log.error(global_PVs['Motor_FurnaceY'].get())
else:
log.info(' *** *** Sample Stack is Frozen')
def adjust_center(params, dark_field, white_field):
global_PVs = aps2bm.init_general_PVs(params)
log.warning(' *** Adjusting center ***')
for ang in [params.adjust_center_angle_1, params.adjust_center_angle_2]:
log.warning(' *** take 3 spheres angular %f deg ***' % float(ang))
#sphere 0
log.info(' *** sphere 0')
log.info(' *** *** moving rotary stage to %f deg position ***' %
float(0))
global_PVs["Motor_SampleRot"].put(float(0), wait=True, timeout=600.0)
log.error(' *** *** acquire sphere at %f deg position ***' %
float(0))
sphere_0 = util.normalize(flir.take_image(global_PVs, params),
white_field, dark_field)
#sphere 1
log.info(' *** sphere 1')
log.info(' *** *** moving rotary stage to %f deg position ***' %
float(ang))
global_PVs["Motor_SampleRot"].put(float(ang), wait=True, timeout=600.0)
log.error(' *** *** acquire sphere at %f deg position ***' %
float(ang))
sphere_1 = util.normalize(flir.take_image(global_PVs, params),
white_field, dark_field)
#sphere 2
log.info(' *** sphere 2')
log.info(' *** *** moving rotary stage to %f deg position ***' %
float(2 * ang))
global_PVs["Motor_SampleRot"].put(float(2 * ang),
wait=True,
timeout=600.0)
log.error(' *** *** acquire sphere at %f deg position ***' %
float(2 * ang))
sphere_2 = util.normalize(flir.take_image(global_PVs, params),
white_field, dark_field)
# find shifts
shift0 = register_translation(sphere_1, sphere_0, 100)[0][1]
shift1 = register_translation(sphere_2, sphere_1, 100)[0][1]
a = ang * np.pi / 180
# x=-(1/4) (d1+d2-2 d1 Cos[a]) Csc[a/2]^2,
x = -(1 / 4) * (shift0 + shift1 - 2 * shift0 * np.cos(a)) * 1 / np.sin(
a / 2)**2
# r = 1/2 Csc[a/2]^2 Csc[a] Sqrt[(d1^2+d2^2-2 d1 d2 Cos[a]) Sin[a/2]^2]
r = 1 / 2 * 1 / np.sin(a / 2)**2 * 1 / np.sin(a) * np.sqrt(
np.abs((shift0**2 + shift1**2 - 2 * shift0 * shift1 * np.cos(a)) *
np.sin(a / 2)**2))
# g = ArcCos[((-d1-d2+2 d1 Cos[a]) Sin[a])/(2 Sqrt[(d1^2+d2^2-2 d1 d2 Cos[a]) Sin[a/2]^2])]
g = np.arccos(
((-shift0 - shift1 + 2 * shift0 * np.cos(a)) * np.sin(a)) /
(2 * np.sqrt(
np.abs(
(shift0**2 + shift1**2 - 2 * shift0 * shift1 * np.cos(a)) *
np.sin(a / 2)**2))))
y = r * np.sin(g) * np.sign(shift0)
# find center of mass
cmass_0 = util.center_of_mass(sphere_0)
log.info(' ')
log.info(
' *** position of the initial sphere wrt to the rotation center (%f,%f) ***'
% (x, y))
log.info(' *** center of mass for the initial sphere (%f,%f) ***' %
(cmass_0[1], cmass_0[0]))
log.info(
' *** moving sphere to the position of the rotation center ***')
if (params.ask):
if util.yes_or_no(' *** Yes or No'):
move_center(params, cmass_0, x, y)
check_center(params, white_field, dark_field)
else:
log.warning(' No motion ')
exit()
else:
move_center(params, cmass_0, x, y)
check_center(params, white_field, dark_field)
def calc_blur_pixel(global_PVs, params):
"""
Calculate the blur error (pixel units) due to a rotary stage fly scan motion durng the exposure.
Parameters
----------
params.exposure_time: float
Detector exposure time
params.ccd_readout : float
Detector read out time
variableDict[''roiSizeX''] : int
Detector X size
params.sample_rotation_end : float
Tomographic scan angle end
params.sample_rotation_start : float
Tomographic scan angle start
variableDict[''Projections'] : int
Numember of projections
Returns
-------
float
Blur error in pixel. For good quality reconstruction this should be < 0.2 pixel.
"""
angular_range = params.sample_rotation_end - params.sample_rotation_start
angular_step = angular_range/params.num_projections
min_scan_time = params.num_projections * (params.exposure_time + params.ccd_readout)
max_rot_speed = angular_range / min_scan_time
max_blur_delta = params.exposure_time * max_rot_speed
mid_detector = global_PVs['Cam1_MaxSizeX_RBV'].get() / 2.0
max_blur_pixel = mid_detector * np.sin(max_blur_delta * np.pi /180.)
max_frame_rate = params.num_projections / min_scan_time
rot_speed = max_rot_speed * params.rotation_slow_factor
scan_time = angular_range / rot_speed
blur_delta = params.exposure_time * rot_speed
mid_detector = global_PVs['Cam1_MaxSizeX_RBV'].get() / 2.0
blur_pixel = mid_detector * np.sin(blur_delta * np.pi /180.)
frame_rate = params.num_projections / scan_time
log.info(' ')
log.info(' *** Calc blur pixel')
log.info(" *** *** Total # of proj: %s " % params.num_projections)
log.info(" *** *** Exposure Time: %s s" % params.exposure_time)
log.info(" *** *** Readout Time: %s s" % params.ccd_readout)
log.info(" *** *** Angular Range: %s degrees" % angular_range)
log.info(" *** *** Camera X size: %s " % global_PVs['Cam1_SizeX'].get())
log.info(' ')
log.info(" *** *** *** *** Angular Step: %4.2f degrees" % angular_step)
log.info(" *** *** *** *** Scan Time: %4.2f (min %4.2f) s" % (scan_time, min_scan_time))
log.info(" *** *** *** *** Rot Speed: %4.2f (max %4.2f) degrees/s" % (rot_speed, max_rot_speed))
log.info(" *** *** *** *** Rot Speed Reduced to: %4.2f %%" % (params.rotation_slow_factor *100.))
log.info(" *** *** *** *** Frame Rate: %4.2f (max %4.2f) fps" % (frame_rate, max_frame_rate))
if (blur_pixel > 1):
log.error(" *** *** *** *** Blur: %4.2f (max %4.2f) pixels" % (blur_pixel, max_blur_pixel))
else:
log.info(" *** *** *** *** Blur: %4.2f (max %4.2f) pixels" % (blur_pixel, max_blur_pixel))
log.info(' *** Calc blur pixel: Done!')
return rot_speed
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
