def fly(global_PVs, params):
angular_range = params.sample_rotation_end - params.sample_rotation_start
flyscan_time_estimate = angular_range / params.slew_speed
log.warning(' *** Fly Scan Time Estimate: %4.2f minutes' % (flyscan_time_estimate/60.))
#Trigger fly motion to start. Don't wait for it, since it takes time.
start_time = time.time()
driver.motor.move(motor_end, wait=False)
time.sleep(1)
old_image_counter = 0
expected_framerate = driver.motor.slew_speed / delta_egu
#Monitor the motion to make sure we aren't stuck.
i = 0
while time.time() - start_time < 1.5 * flyscan_time_estimate:
i += 1
if i % 10 == 0:
log.info(' *** *** Sample rotation at angle {:f}'.format(driver.motor.readback))
time.sleep(1)
if not driver.motor.moving:
log.info(' *** *** Sample rotation stopped moving.')
if abs(driver.motor.drive - motor_end) > 1e-2:
log.error(' *** *** Sample rotation ended but not at right position!')
raise ValueError
else:
log.info(' *** *** Stopped at correct position.')
break
#Make sure we're actually getting frames.
current_image_counter = global_PVs['Cam1_NumImagesCounter'].get()
if current_image_counter - old_image_counter < 0.2 * expected_framerate:
log.error(' *** *** Not collecting frames!')
raise ValueError
else:
old_image_counter = current_image_counter
else:
log.warning(' *** *** Fly motion timed out!')
raise ValueError
def find_roll_and_rotation_axis_location(params):
global_PVs = aps7bm.init_general_PVs(params)
params.file_name = None # so we don't run the flir._setup_hdf_writer
try:
if not scan.check_camera_IOC(global_PVs, params):
return False
flir.init(global_PVs, params)
flir.set(global_PVs, params)
sphere_0, sphere_180 = take_sphere_0_180(global_PVs, params)
cmass_0 = center_of_mass(sphere_0)
cmass_180 = center_of_mass(sphere_180)
params.rotation_axis_position = (cmass_180[1] + cmass_0[1]) / 2.0
log.info(' *** shift (center of mass): [%f, %f]' %
((cmass_180[0] - cmass_0[0]),
(cmass_180[1] - cmass_0[1])))
params.roll = np.rad2deg(
np.arctan(
(cmass_180[0] - cmass_0[0]) / (cmass_180[1] - cmass_0[1])))
log.info(" *** roll:%f" % (params.roll))
config.update_sphere(params)
return params.rotation_axis_position, params.roll
except KeyError:
log.error(' *** Some PV assignment failed!')
pass
def set(global_PVs, params):
'''Sets up detector and arms it for PSO pulses.
'''
fname = params.file_name
# Set detectors
if params.camera_ioc_prefix in params.valid_camera_prefixes:
log.info(' ')
log.info(' *** setup Point Grey')
# Make sure that we aren't acquiring now
global_PVs['Cam1_Acquire'].put(DetectorIdle)
aps7bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle)
#Set up the XML files to determine HDF file layout
attrib_file = Path.joinpath(
Path(__file__).parent, 'mctDetectorAttributes1.xml')
global_PVs['Cam1_AttributeFile'].put(str(attrib_file), wait=True)
layout_file = Path.joinpath(Path(__file__).parent, 'mct3.xml')
global_PVs['HDF1_XMLFileName'].put(str(layout_file), wait=True)
global_PVs['Cam1_ArrayCallbacks'].put('Enable', wait=True)
global_PVs['Cam1_AcquirePeriod'].put(float(params.exposure_time),
wait=True)
global_PVs['Cam1_AcquireTime'].put(float(params.exposure_time),
wait=True)
log.info(' *** setup Point Grey: Done!')
else:
log.error('Detector %s is not defined' % params.camera_ioc_prefix)
return
if params.file_name is None:
log.warning(' *** hdf_writer will not be configured')
else:
_setup_hdf_writer(global_PVs, params, fname)
def stop_scan(global_PVs, params):
log.info(' ')
log.error(' *** Stopping the scan: PLEASE WAIT')
aps7bm.close_shutters(global_PVs, params)
global_PVs['Motor_SampleRot'].stop()
global_PVs['HDF1_Capture'].put(0)
aps7bm.wait_pv(global_PVs['HDF1_Capture'], 0)
pso.cleanup_PSO()
flir.init(global_PVs, params)
log.error(' *** Stopping scan: Done!')
def _setup_hdf_writer(global_PVs, params, fname=None):
if params.camera_ioc_prefix in params.valid_camera_prefixes:
# 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['Cam1_AsynPort'].get(),
wait=True)
global_PVs['HDF1_AutoSave'].put('Yes')
global_PVs['HDF1_DeleteDriverFile'].put('No')
global_PVs['HDF1_EnableCallbacks'].put('Enable', wait=True)
global_PVs['HDF1_BlockingCallbacks'].put('No')
totalProj = (int(params.num_projections) +
int(params.num_dark_images) +
int(params.num_white_images))
global_PVs['HDF1_NumCapture'].put(totalProj, wait=True)
global_PVs['HDF1_ExtraDimSizeN'].put(totalProj, wait=True)
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)
aps7bm.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 fly_scan(params):
'''Perform potentially repeated fly scan.
'''
tic = time.time()
global_PVs = aps7bm.init_general_PVs(params)
try:
if not check_camera_IOC(global_PVs, params):
return False
# Set the slew speed, possibly based on blur and acquisition parameters
set_slew_speed(global_PVs, params)
# init camera
flir.init(global_PVs, params)
log.info(' ')
log.info(" *** Running %d sleep scans" % params.sleep_steps)
for i in np.arange(params.sleep_steps):
tic_01 = time.time()
# 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)
log.info(' ')
log.info(' *** Start scan {:d} of {:d}'.format(
int(i + 1), int(params.sleep_steps)))
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.))
global_PVs['Cam1_ImageMode'].put('Continuous')
log.info(' *** Done!')
except KeyError:
log.error(' *** Some PV assignment failed!')
except Exception as ee:
stop_scan(global_PVs, params)
log.info(' Exception recorded: ' + str(ee))
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.info(args.file_path)
log.info(args.file_name)
log_fname = str(Path.joinpath(Path(args.file_path), 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))
def dummy_scan(params):
tic = time.time()
# aps7bm.update_variable_dict(params)
global_PVs = aps7bm.init_general_PVs(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 acquire_dark(global_PVs, params):
log.info(' *** Dark Fields')
# Make sure that we aren't acquiring now
global_PVs['Cam1_Acquire'].put(DetectorIdle)
aps7bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle)
global_PVs['Cam1_ImageMode'].put('Multiple', wait=True)
global_PVs['Cam1_FrameType'].put(FrameTypeDark, wait=True)
global_PVs['Cam1_TriggerMode'].put('Internal', wait=True)
num_images = int(
params.num_white_images) * params.recursive_filter_n_images
global_PVs['Cam1_NumImages'].put(num_images, wait=True)
wait_time = int(num_images) * params.exposure_time + 5
global_PVs['Cam1_Acquire'].put(DetectorAcquire)
time.sleep(1.0)
if aps7bm.wait_pv(global_PVs['Cam1_Acquire'], DetectorIdle, wait_time):
log.info(' *** Dark Fields: Done!')
else:
log.error(' *** *** Timeout.')
raise Exception
def find_tilt_rotation_axis(params):
global_PVs = aps7bm.init_general_PVs(params)
params.file_name = None # so we don't run the flir._setup_hdf_writer
try:
if not scan.check_camera_IOC(global_PVs, params):
return False
flir.init(global_PVs, params)
flir.set(global_PVs, params)
sphere_0, sphere_180 = take_sphere_0_180(global_PVs, params)
sphere_180_flip = sphere_180[..., ::-1]
#Find pixel shift between images
log.info(' *** Calculating shift. This will take a minute.')
shifts, error, phasediff = register_translation(
sphere_0, sphere_180_flip, 10)
log.info(' *** Calculated shift is ({0:6.4f}, {1:6.4f})'.format(
shifts[0], shifts[1]))
overall_res = float(global_PVs['PixelSizeMicrons'].get()) / float(
params.lens_magnification)
log.info(' *** Rotation axis off by {0:6.4} mm'.format(
shifts[1] * overall_res / 2e3))
log.info(' *** Move SampleX by {0:6.4} mm'.format(shifts[1] *
overall_res / 2e3))
log.info(' *** Shift in Y = {0:6.4} microns'.format(shifts[0] *
overall_res))
tilt_angle = np.degrees(shifts[0] * overall_res / 25.4 / 1e3)
log.info(' *** Equivalent to {0:6.4} deg'.format(tilt_angle))
#Plot the shifted image
sphere_1 = np.roll(sphere_180_flip, (int(shifts[0]), int(shifts[1])),
axis=(0, 1))
plt.figure(2)
plt.imshow((sphere_0 - sphere_1)[abs(int(shifts[0])):,
abs(int(shifts[1])):],
vmin=-0.1,
vmax=0.1)
plt.colorbar()
plt.title('Difference image after shift')
plt.show()
return 0, 0
except KeyError:
log.error(' *** Some PV assignment failed!')
def checkclose_hdf(global_PVs, params):
''' Check if the HDF5 file has closed. Will wait for data to flush to disk.
'''
buffer_queue = global_PVs['HDF1_QueueSize'].get(
) - global_PVs['HDF1_QueueFree'].get()
frate = 55.0
wait_on_hdd = buffer_queue / frate + 10
log.info(' *** Buffer Queue (frames): %d ' % buffer_queue)
log.info(' *** Wait HDD (s): %f' % wait_on_hdd)
if aps7bm.wait_pv(
global_PVs["HDF1_Capture_RBV"], 0, wait_on_hdd
) == False: # needs to wait for HDF plugin queue to dump to disk
global_PVs["HDF1_Capture"].put(0)
log.info(' *** File was not closed => forced to close')
log.info(' *** before %d' % global_PVs["HDF1_Capture_RBV"].get())
aps7bm.wait_pv(global_PVs["HDF1_Capture_RBV"], 0, 5)
log.info(' *** after %d' % global_PVs["HDF1_Capture_RBV"].get())
if (global_PVs["HDF1_Capture_RBV"].get() == 1):
log.error(
' *** ERROR HDF FILE DID NOT CLOSE; add_theta will fail')
def move_sample_in(global_PVs, params):
log.info(' *** Sample in')
if params.sample_move_freeze:
log.info(' *** *** Sample motion is frozen.')
return
try:
#If we haven't saved original positions yet, use the current ones.
try:
_ = params.original_x
_ = params.original_y
except AttributeError:
params.original_x = global_PVs['Motor_SampleX'].drive
params.original_y = global_PVs['Motor_SampleY'].drive
log.info(' *** Moving to (x,y) = ({0:6.4f}, {1:6.4f})'.format(
params.original_x, params.original_y))
#Check the limits
if not (global_PVs['Motor_SampleX'].within_limits(params.original_x)
and global_PVs['Motor_SampleY'].within_limits(
params.original_y)):
log.error(' *** *** Sample in position past motor limits.')
return
global_PVs['Motor_SampleX'].move(params.original_x,
wait=True,
timeout=10)
global_PVs['Motor_SampleY'].move(params.original_y,
wait=True,
timeout=10)
#Check if we ever got there
if (abs(global_PVs['Motor_SampleX'].readback - params.original_x) >
1e-3 or abs(global_PVs['Motor_SampleY'].readback -
params.original_y) > 1e-3):
log.error(' *** *** Sample in motion failed!')
except Exception as ee:
log.error('EXCEPTION DURING SAMPLE IN MOTION!')
raise ee
def move_sample_out(global_PVs, params):
log.info(' *** Sample out')
if params.sample_move_freeze:
log.info(' *** *** Sample motion is frozen.')
return
params.original_x = global_PVs['Motor_SampleX'].drive
params.original_y = global_PVs['Motor_SampleY'].drive
try:
#Check the limits
out_x = params.sample_out_x
out_y = params.sample_out_y
log.info(' *** Moving to (x,y) = ({0:6.4f}, {1:6.4f})'.format(
out_x, out_y))
if not (global_PVs['Motor_SampleX'].within_limits(out_x)
and global_PVs['Motor_SampleY'].within_limits(out_y)):
log.error(' *** *** Sample out position past motor limits.')
return
global_PVs['Motor_SampleX'].move(out_x, wait=True, timeout=10)
global_PVs['Motor_SampleY'].move(out_y, wait=True, timeout=10)
#Check if we ever got there
time.sleep(0.2)
if (abs(global_PVs['Motor_SampleX'].readback - out_x) > 1e-3
or abs(global_PVs['Motor_SampleY'].readback - out_y) > 1e-3):
log.error(' *** *** Sample out motion failed!')
except Exception as ee:
log.error('EXCEPTION DURING SAMPLE OUT MOTION!')
global_PVs['Motor_SampleX'].move(params.original_x,
wait=True,
timeout=10)
global_PVs['Motor_SampleY'].move(params.original_y,
wait=True,
timeout=10)
raise ee
def wait_pv(pv, wait_val, max_timeout_sec=-1):
''' Wait on a PV to reach a value.
max_timeout_sec is an optional timeout time.
'''
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_vertical(params):
tic = time.time()
# aps7bm.update_variable_dict(params)
global_PVsx = aps7bm.init_general_PVs(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'
blur_pixel, rot_speed, scan_time = 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
# init camera
flir.init(global_PVs, params)
log.info(' ')
log.info(" *** Running %d scans" % params.sleep_steps)
log.info(' ')
log.info(' *** Vertical Positions (mm): %s' %
np.arange(start_y, end_y, step_size_y))
for ii in np.arange(0, params.sleep_steps, 1):
log.info(' ')
log.info(' *** Start scan %d' % ii)
for i in np.arange(start_y, end_y, step_size_y):
tic_01 = time.time()
# 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)
log.info(' ')
log.info(' *** The sample vertical position is at %s mm' %
(i))
global_PVs['Motor_SampleY'].put(i,
wait=True,
timeout=1000.0)
tomo_fly_scan(global_PVs, params)
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(' *** Moving vertical stage to start position')
global_PVs['Motor_SampleY'].put(start_y,
wait=True,
timeout=1000.0)
if ((ii + 1) != params.sleep_steps):
log.warning(' *** Wait (s): %s ' % str(params.sleep_time))
time.sleep(params.sleep_time)
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(0, 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 init_general_PVs(params):
'''Initialize epics PV objects.
'''
global_PVs = {}
log.info('Creating PV objects.')
# shutter pv's
global_PVs['ShutterA_Open'] = PV('7bma1:rShtrA:Open')
global_PVs['ShutterA_Close'] = PV('7bma1:rShtrA:Close')
global_PVs['ShutterA_Move_Status'] = PV('PB:07BM:STA_A_FES_CLSD_PL.VAL')
# Experimment Info
global_PVs['Sample_Name'] = PV('7bmb1:ExpInfo:SampleName')
global_PVs['Sample_Description'] = PV(
'7bmb1:ExpInfo:SampleDescription.VAL')
global_PVs['User_Badge'] = PV('7bmb1:ExpInfo:UserBadge.VAL')
global_PVs['User_Email'] = PV('7bmb1:ExpInfo:UserEmail.VAL')
global_PVs['User_Institution'] = PV('7bmb1:ExpInfo:UserInstitution.VAL')
global_PVs['Proposal_Number'] = PV('7bmb1:ExpInfo:ProposalNumber.VAL')
global_PVs['Proposal_Title'] = PV('7bmb1:ExpInfo:ProposalTitle.VAL')
global_PVs['User_Info_Update'] = PV('7bmb1:ExpInfo:UserInfoUpdate.VAL')
global_PVs['Lens_Magnification'] = PV('7bmb1:ExpInfo:LensMagFloat.VAL')
global_PVs['Scintillator_Type'] = PV('7bmb1:ExpInfo:ScintillatorType.VAL')
global_PVs['Scintillator_Thickness'] = PV(
'7bmb1:ExpInfo:ScintillatorThickness.VAL')
global_PVs['Camera_IOC_Prefix'] = PV('7bmb1:ExpInfo:CameraIOCPrefix.VAL')
global_PVs['PixelSizeMicrons'] = PV('7bmb1:ExpInfo:PixelSizeum.VAL')
global_PVs['Filters'] = PV('7bmb1:ExpInfo:Filters.VAL')
global_PVs['File_Name'] = PV('7bmb1:ExpInfo:FileName.VAL')
global_PVs['Station'] = PV('7bmb1:ExpInfo:Station.VAL')
global_PVs['Remote_Data_Trasfer'] = PV(
'7bmb1:ExpInfo:RemoteDataTrasfer.VAL')
global_PVs['Remote_Analysis_Dir'] = PV(
'7bmb1:ExpInfo:RemoteAnalysisDir.VAL')
global_PVs['User_Last_Name'] = PV('7bmb1:ExpInfo:UserLastName.VAL')
global_PVs['Experiment_Year_Month'] = PV(
'7bmb1:ExpInfo:ExperimentYearMonth.VAL')
global_PVs['Use_Furnace'] = PV('7bmb1:ExpInfo:UseFurnace.VAL')
global_PVs['White_Field_Motion'] = PV('7bmb1:ExpInfo:WhiteFieldMotion.VAL')
global_PVs['Num_White_Images'] = PV('7bmb1:ExpInfo:NumWhiteImages.VAL')
global_PVs['Bright_Exp_Time'] = PV('7bmb1:ExpInfo:BrightExposureTime.VAL')
global_PVs['Sample_Detector_Distance'] = PV(
'7bmb1:ExpInfo:SampleDetectorDistance.VAL')
global_PVs['Sample_Out_Position_Y'] = PV(
'7bmb1:ExpInfo:SampleOutPositionY.VAL')
global_PVs['Sample_Out_Position_X'] = PV(
'7bmb1:ExpInfo:SampleOutPositionX.VAL')
global_PVs['Num_Projections'] = PV('7bmb1:ExpInfo:NumProjections.VAL')
global_PVs['Sample_Rotation_Start'] = PV(
'7bmb1:ExpInfo:SampleRotationStart.VAL')
global_PVs['Sample_Rotation_End'] = PV(
'7bmb1:ExpInfo:SampleRotationEnd.VAL')
global_PVs['Sample_Rotation_Speed'] = PV(
'7bmb1:ExpInfo:SampleRotationSpeed.VAL')
global_PVs['Sample_Retrace_Speed'] = PV('7bmb1:ExpInfo:RetraceSpeed.VAL')
global_PVs['Furnace_In_Position'] = PV(
'7bmb1:ExpInfo:FurnaceInPosition.VAL')
global_PVs['Furnace_Out_Position'] = PV(
'7bmb1:ExpInfo:FurnaceOutPosition.VAL')
global_PVs['Scan_Type'] = PV('7bmb1:ExpInfo:ScanType.VAL')
global_PVs['Sleep_Time'] = PV('7bmb1:ExpInfo:SleepTime.VAL')
global_PVs['Scan_Replicates'] = PV('7bmb1:ExpInfo:ScanReplicates.VAL')
global_PVs['Vertical_Scan_Start'] = PV(
'7bmb1:ExpInfo:VerticalScanStart.VAL')
global_PVs['Vertical_Scan_End'] = PV('7bmb1:ExpInfo:VerticalScanEnd.VAL')
global_PVs['Vertical_Scan_Step_Size'] = PV(
'7bmb1:ExpInfo:VerticalScanStepSize.VAL')
global_PVs['Horizontal_Scan_Start'] = PV(
'7bmb1:ExpInfo:HorizontalScanStart.VAL')
global_PVs['Horizontal_Scan_End'] = PV(
'7bmb1:ExpInfo:HorizontalScanEnd.VAL')
global_PVs['Horizontal_Scan_Step_Size'] = PV(
'7bmb1:ExpInfo:HorizontalScanStepSize.VAL')
params.station = global_PVs['Station'].get(as_string=True)
log.info('Running in station {:s}.'.format(params.station))
if params.station == '7-BM-B':
log.info('*** Running in station 7-BM-B:')
# Set sample stack motor:
global_PVs['Motor_SampleX'] = Motor('7bmb1:aero:m2')
global_PVs['Motor_SampleY'] = Motor('7bmb1:aero:m1')
global_PVs['Motor_SampleRot'] = Motor(
'7bmb1:aero:m3') # Aerotech ABR-250
global_PVs['Motor_Focus'] = Motor('7bmb1:m38')
else:
log.error('*** %s is not a valid station' % params.station)
# detector pv's
params.valid_camera_prefixes = [
'7bm_pg1:', '7bm_pg2:', '7bm_pg3:', '7bm_pg4:'
]
params.camera_ioc_prefix = global_PVs['Camera_IOC_Prefix'].get(
as_string=True)
if params.camera_ioc_prefix[-1] != ':':
params.camera_ioc_prefix = params.camera_ioc_prefix + ':'
log.info('Using camera IOC with prefix {:s}'.format(
params.camera_ioc_prefix))
if params.camera_ioc_prefix in params.valid_camera_prefixes:
update_pixel_size(global_PVs, params)
# init Point Grey PV's
# general PV's
global_PVs['Cam1_SerialNumber'] = PV(params.camera_ioc_prefix +
'cam1:SerialNumber')
global_PVs['Cam1_AsynPort'] = PV(params.camera_ioc_prefix +
'cam1:PortName_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_NumImagesCounter'] = PV(params.camera_ioc_prefix +
'cam1:NumImagesCounter_RBV')
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_Dtype'] = PV(params.camera_ioc_prefix +
'image1:DataType_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_ExtraDimSizeN'] = PV(params.camera_ioc_prefix +
'HDF1:ExtraDimSizeN')
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')
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
global TESTING
TESTING = params.testing
user_info_update(global_PVs, params)
if params.update_from_PVs:
update_params_from_PVs(global_PVs, params)
return global_PVs
def find_resolution(params):
log.info('find resolution')
global_PVs = aps7bm.init_general_PVs(params)
aps7bm.user_info_update(global_PVs, params)
params.file_name = None # so we don't run the flir._setup_hdf_writer
try:
if not scan.check_camera_IOC(global_PVs, params):
return False
flir.init(global_PVs, params)
flir.set(global_PVs, params)
dark_field, white_field = flir.take_dark_and_white(
global_PVs, params, True)
start_position = global_PVs["Motor_SampleX"].drive
log.info(' *** First image at X: %f mm' % (start_position))
log.info(' *** acquire first image')
sphere_0 = flir.take_image(global_PVs, params)
second_image_x_position = start_position + params.off_axis_position
log.info(' *** Second image at X: %f mm' % (second_image_x_position))
global_PVs["Motor_SampleX"].move(second_image_x_position,
wait=True,
timeout=600.0)
time.sleep(0.5)
log.info(' *** acquire second image')
sphere_1 = flir.take_image(global_PVs, params)
log.info(' *** moving X stage back to %f mm position' %
(start_position))
aps7bm.close_shutters(global_PVs, params)
global_PVs["Motor_SampleX"].move(start_position, wait=True)
sphere_0 = normalize(sphere_0, white_field, dark_field)
sphere_1 = normalize(sphere_1, white_field, dark_field)
log.info(' *** images normalized and unsharp masked')
plt.imshow(sphere_0 - sphere_1) #, vmin=-4, vmax=4)
plt.colorbar()
plt.title('Difference image 1 - 2')
#Find pixel shift between images
log.info(' *** Calculating shift. This will take a minute.')
shifts, error, phasediff = register_translation(sphere_0, sphere_1, 10)
log.info(' *** Calculated shift is ({0:6.4f}, {1:6.4f})'.format(
shifts[0], shifts[1]))
total_shift = np.hypot(shifts[0], shifts[1])
log.info(' *** total shift {:6.4f} pixels'.format(total_shift))
pixel_size = float(global_PVs['PixelSizeMicrons'].get())
log.info(' *** pixel size = {:6.4f} microns'.format(pixel_size))
params.lens_magnification = abs(
float(total_shift) * pixel_size / params.off_axis_position / 1e3)
if params.auto_magnification:
global_PVs['Lens_Magnification'].put(params.lens_magnification)
#Plot the shifted image
sphere_1 = np.roll(sphere_1, (int(shifts[0]), int(shifts[1])),
axis=(0, 1))
plt.figure(2)
plt.imshow((sphere_0 - sphere_1)[abs(int(shifts[0])):,
abs(int(shifts[1])):])
plt.colorbar()
plt.title('Difference image after shift')
plt.show()
config.update_sphere(params)
return params.resolution
except KeyError:
log.error(' *** Some PV assignment failed!')
pass
