def tune_usaxs_optics(side=False, md={}):
"""
tune all the instrument optics currently in configuration
This plan is for staff use.
Users are advised to use preUSAXStune() instead.
"""
yield from mode_USAXS()
suspender_preinstalled = suspend_BeamInHutch in RE.suspenders
if not suspender_preinstalled:
yield from bps.install_suspender(suspend_BeamInHutch)
yield from tune_mr(md=md)
yield from tune_m2rp(md=md)
if side:
yield from tune_msrp(md=md)
yield from tune_asrp(md=md)
yield from tune_ar(md=md)
yield from tune_a2rp(md=md)
if not suspender_preinstalled:
yield from bps.remove_suspender(suspend_BeamInHutch)
yield from bps.mv(
terms.preUSAXStune.num_scans_last_tune,
0,
terms.preUSAXStune.epoch_last_tune,
time.time(),
)
def scan_closure():
# open shutter for beam
yield from bps.mv(shutter, 'open')
yield from bps.install_suspender(shutter_suspender)
# config output
for me in [det.tiff1, det.hdf1]:
yield from bps.mv(me.file_path, fp)
yield from bps.mv(me.file_name, fn)
yield from bps.mv(me.file_write_mode, 2)
yield from bps.mv(me.num_capture, total_images)
yield from bps.mv(
me.file_template,
".".join([r"%s%s_%06d", cfg['output']['type'].lower()]))
if cfg['output']['type'] in ['tif', 'tiff']:
yield from bps.mv(det.tiff1.enable, 1)
yield from bps.mv(det.tiff1.capture, 1)
yield from bps.mv(det.hdf1.enable, 0)
elif cfg['output']['type'] in ['hdf', 'hdf1', 'hdf5']:
yield from bps.mv(det.tiff1.enable, 0)
yield from bps.mv(det.hdf1.enable, 1)
yield from bps.mv(det.hdf1.capture, 1)
else:
raise ValueError(
f"Unsupported output type {cfg['output']['type']}")
# collect front white field
yield from bps.mv(det.cam.frame_type,
0) # for HDF5 dxchange data structure
yield from collect_white_field(experiment, cfg['tomo'], atfront=True)
# collect projections
yield from bps.mv(det.cam.frame_type,
1) # for HDF5 dxchange data structure
if cfg['tomo']['type'].lower() == 'step':
yield from step_scan(experiment, cfg['tomo'])
elif cfg['tomo']['type'].lower() == 'fly':
yield from fly_scan(experiment, cfg['tomo'])
else:
raise ValueError(f"Unsupported scan type: {cfg['tomo']['type']}")
# collect back white field
yield from bps.mv(det.cam.frame_type,
2) # for HDF5 dxchange data structure
yield from collect_white_field(experiment, cfg['tomo'], atfront=False)
# collect back dark field
yield from bps.mv(det.cam.frame_type,
3) # for HDF5 dxchange data structure
yield from bps.remove_suspender(shutter_suspender)
yield from bps.mv(shutter, "close")
yield from collect_dark_field(experiment, cfg['tomo'])
def imprint_row(*args, events=1, min_mj=0.5):
"""
Run a single row of the imprint scan
Parameters
----------
args: passed to bluesky.plans.scan
events: int
The number of events to allow at each stopping point in the scan
min_mj, float, optional
The minimum energy the scan should continue to execute scans
Example
-------
.. code::
# Run a scan from -1, 1 in 10 steps with 40 shots at each step
RE(imprint_row(pi_x, -1, 1, 10, events=40))
# Run a scan with two motors from -1, 1 and 12, 20, in five steps with
# 10 shots at each step. Pause if we have less than 1 mJ in the GDET
RE(imprint_row(pi_x, -1, 1,
cxi.kb2.hl, 12, 20, 5,
events=10, min_mj=1))
"""
# Create a new suspender
suspender = SuspendFloor(beam_stats.mj_avg, min_mj)
# Install the new suspender
yield from bps.install_suspender(suspender)
# Execute a scan first configuring the Sequencer and DAQ
try:
yield from sequencer_mode(daq, sequencer, events, sequence_wait=.25)
yield from bp.scan([daq, sequencer], *args)
# Always ensure we remove the suspender
finally:
yield from bps.remove_suspender(suspender)
def scan_closure():
# -------------------
# collect white field
# -------------------
# 1-1 monitor shutter status, auto-puase scan if beam is lost
yield from bps.open_run()
yield from bps.mv(A_shutter, 'open')
yield from bps.install_suspender(suspend_A_shutter)
#1-1.5 configure output plugins edited by Jason 07/19/2019
for me in [det.tiff1, det.hdf1]:
yield from bps.mv(me.file_path, fp)
yield from bps.mv(me.file_name, fn)
yield from bps.mv(me.file_write_mode, 2)
yield from bps.mv(me.num_capture, total_images)
yield from bps.mv(
me.file_template,
".".join([r"%s%s_%06d", config['output']['type'].lower()]))
if config['output']['type'] in ['tif', 'tiff']:
yield from bps.mv(det.tiff1.enable, 1)
yield from bps.mv(det.tiff1.capture, 1)
yield from bps.mv(det.hdf1.enable, 0)
elif config['output']['type'] in ['hdf', 'hdf1', 'hdf5']:
yield from bps.mv(det.tiff1.enable, 0)
yield from bps.mv(det.hdf1.enable, 1)
yield from bps.mv(det.hdf1.capture, 1)
else:
raise ValueError(f"Unsupported output type {output_dict['type']}")
# 1-2 move sample out of the way
initial_samx = samX.position
initial_samy = samY.position
initial_preci = preci.position
dx = config['tomo']['sample_out_position']['samX']
dy = config['tomo']['sample_out_position']['samY']
r = config['tomo']['sample_out_position']['preci']
yield from bps.mv(samX, initial_samx + dx)
yield from bps.mv(samY, initial_samy + dy)
yield from bps.mv(preci, r)
# 1-2.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 0)
# 1-3 collect front white field images
yield from bps.mv(det.hdf1.nd_array_port, 'PROC1')
yield from bps.mv(det.tiff1.nd_array_port, 'PROC1')
yield from bps.mv(det.proc1.enable, 1)
yield from bps.mv(det.proc1.reset_filter, 1)
yield from bps.mv(det.proc1.num_filter, n_frames)
yield from bps.mv(det.cam.trigger_mode, "Internal")
yield from bps.mv(det.cam.image_mode, "Multiple")
yield from bps.mv(det.cam.num_images, n_frames * n_white)
yield from bps.mv(det.cam.acquire_time, acquire_time)
yield from bps.mv(det.cam.acquire_period, acquire_period)
yield from bps.trigger_and_read([det])
# 1-4 move sample back
yield from bps.mv(samX, initial_samx)
yield from bps.mv(samY, initial_samy)
#yield from bps.mv(preci, initial_preci)
# -------------------
# collect projections
# -------------------
# 1-5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 1)
# 1-6 step and fly scan are differnt
if config['tomo']['type'].lower() == 'step':
yield from bps.mv(det.proc1.reset_filter, 1)
yield from bps.mv(det.cam.num_images, n_frames)
# 1-6 collect projections
for ang in angs:
yield from bps.checkpoint()
yield from bps.mv(preci, ang)
yield from bps.trigger_and_read([det])
elif config['tomo']['type'].lower() == 'fly':
yield from bps.mv(det.proc1.num_filter, 1)
yield from bps.mv(det.hdf1.nd_array_port, 'PG1')
yield from bps.mv(det.tiff1.nd_array_port, 'PG1')
yield from bps.mv(
psofly.start,
config['tomo']['omega_start'],
psofly.end,
config['tomo']['omega_end'],
psofly.scan_delta,
abs(config['tomo']['omega_step']),
psofly.slew_speed,
slew_speed,
)
# taxi
yield from bps.mv(psofly.taxi, "Taxi")
# setup detector to overlap for fly scan
yield from bps.mv(
det.cam.num_images,
n_projections,
det.cam.trigger_mode,
"Overlapped",
)
# start the fly scan
print("before trigger")
yield from bps.trigger(det, group='trigger')
print("waiting for trigger")
# yield from bps.wait(group='trigger')
print("before plan()")
try:
yield from psofly.plan()
except NotEnoughTriggers as err:
reason = (
f"{err.expected:.0f} were expected but {err.actual:.0f} were received."
)
yield from bps.close_run('fail', reason=reason)
return # short-circuit
# fly scan finished. switch image port and trigger_mode back
yield from bps.mv(det.cam.trigger_mode, "Internal")
yield from bps.mv(det.hdf1.nd_array_port, 'PROC1')
yield from bps.mv(det.tiff1.nd_array_port, 'PROC1')
else:
raise ValueError(f"Unknown scan type: {config['tomo']['type']}")
# ------------------
# collect back white
# ------------------
# 1-7 move the sample out of the way
# NOTE:
# this will return ALL motors to starting positions, we need a
# smart way to calculate a shorter trajectory to move sample
# out of way
yield from bps.mv(preci, r)
yield from bps.mv(samX, initial_samx + dx)
yield from bps.mv(samY, initial_samy + dy)
# 1-7.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 2)
# 1-8 take the back white
yield from bps.mv(det.proc1.num_filter, n_frames)
yield from bps.mv(det.cam.num_images, n_frames * n_white)
yield from bps.trigger_and_read([det])
# 1-9 move sample back
yield from bps.mv(samX, initial_samx)
yield from bps.mv(samY, initial_samy)
# -----------------
# collect back dark
# -----------------
# 1-10 close the shutter
yield from bps.remove_suspender(suspend_A_shutter)
yield from bps.mv(A_shutter, "close")
# 1-10.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 3)
# 1-11 collect the back dark
yield from bps.mv(det.cam.num_images, n_frames * n_dark)
yield from bps.trigger_and_read([det])
yield from bps.close_run('success')
def scan_closure():
yield from bps.mv(det.cam.acquire_time, acquire_time)
yield from bps.mv(det.cam.acquire_period, acquire_period)
# -------------------
# collect white field
# -------------------
# 1-1 monitor shutter status, auto-puase scan if beam is lost
yield from bps.mv(A_shutter, 'open')
yield from bps.install_suspender(suspend_A_shutter)
# 1-2 move sample out of the way
current_samx = samx.position
current_samy = samy.position
current_preci = preci.position
dx = config['tomo']['sample_out_position']['samx']
dy = config['tomo']['sample_out_position']['samy']
dr = config['tomo']['sample_out_position']['preci']
yield from bps.mv(samx, current_samx + dx)
yield from bps.mv(samy, current_samy + dy)
yield from bps.mv(preci, current_preci + dr)
# 1-2.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 0)
# 1-3 collect front white field images
yield from bps.mv(det.proc1.enable, 1)
yield from bps.mv(det.proc1.reset_filter, 1)
yield from bps.mv(det.proc1.num_filter, n_frames)
yield from bps.mv(det.cam.trigger_mode, "Internal")
yield from bps.mv(det.cam.image_mode, "Multiple")
yield from bps.mv(det.cam.num_images, n_frames * n_white)
yield from bps.trigger_and_read([det])
# 1-4 move sample back
yield from bps.mv(samx, current_samx)
yield from bps.mv(samy, current_samy)
yield from bps.mv(preci, current_preci)
# -------------------
# collect projections
# -------------------
# 1-4.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 1)
# 1-5 quicly reset proc1
yield from bps.mv(det.proc1.reset_filter, 1)
yield from bps.mv(det.cam.num_images, n_frames)
# 1-6 collect projections
for ang in angs:
yield from bps.checkpoint()
yield from bps.mv(preci, ang)
yield from bps.trigger_and_read([det])
# ------------------
# collect back white
# ------------------
# 1-7 move the sample out of the way
# NOTE:
# this will return ALL motors to starting positions, we need a
# smart way to calculate a shorter trajectory to move sample
# out of way
yield from bps.mv(preci, current_preci + dr)
yield from bps.mv(samx, current_samx + dx)
yield from bps.mv(samy, current_samy + dy)
# 1-7.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 2)
# 1-8 take the back white
yield from bps.mv(det.cam.num_images, n_frames * n_white)
yield from bps.trigger_and_read([det])
# 1-9 move sample back
yield from bps.mv(samx, current_samx)
yield from bps.mv(samy, current_samy)
yield from bps.mv(preci, current_preci)
# -----------------
# collect back dark
# -----------------
# 1-10 close the shutter
yield from bps.remove_suspender(suspend_A_shutter)
yield from bps.mv(A_shutter, "close")
# 1-10.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 3)
# 1-11 collect the back dark
yield from bps.mv(det.cam.num_images, n_frames * n_dark)
yield from bps.trigger_and_read([det])
def scan_closure():
yield from bps.mv(det.cam.acquire_time, acquire_time)
yield from bps.mv(det.cam.acquire_period, acquire_period)
# -------------------
# collect white field
# -------------------
# 1-1 monitor shutter status, auto-puase scan if beam is lost
yield from bps.mv(A_shutter, 'open')
yield from bps.install_suspender(suspend_A_shutter)
# 1-2 move sample out of the way
current_samx = samx.position
current_samy = samy.position
current_preci = preci.position
dx = config['tomo']['sample_out_position']['samx']
dy = config['tomo']['sample_out_position']['samy']
dr = config['tomo']['sample_out_position']['preci']
yield from bps.mv(samx, current_samx + dx)
yield from bps.mv(samy, current_samy + dy)
yield from bps.mv(preci, current_preci + dr)
# 1-2.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 0)
# 1-3 collect front white field images
yield from bps.mv(det.proc1.enable, 1)
yield from bps.mv(det.proc1.reset_filter, 1)
yield from bps.mv(det.proc1.num_filter, n_frames)
yield from bps.mv(det.cam.trigger_mode, "Internal")
yield from bps.mv(det.cam.image_mode, "Multiple")
yield from bps.mv(det.cam.num_images, n_frames * n_white)
yield from bps.trigger_and_read([det])
# 1-4 move sample back
yield from bps.mv(samx, current_samx)
yield from bps.mv(samy, current_samy)
yield from bps.mv(preci, current_preci)
# -------------------
# collect projections
# -------------------
# 1-4.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 1)
# 1-5 quicly reset proc1
yield from bps.mv(det.proc1.reset_filter, 1)
# 1-6 collect projections
yield from motor_set_modulo(preci, 360.0)
# configure the psofly interface
yield from bps.mv(
psofly.start,
config['tomo']['omega_start'],
psofly.end,
config['tomo']['omega_end'],
psofly.scan_control,
"Standard",
psofly.scan_delta,
config['tomo']['omega_step'],
psofly.slew_speed,
slew_speed,
preci.velocity,
ROT_STAGE_FAST_SPEED,
preci.acceleration,
slew_speed / accl,
)
# taxi
yield from bps.mv(psofly.taxi, "Taxi")
yield from bps.mv(preci.velocity, slew_speed)
# ???
yield from bps.mv(
det.cam.num_images,
n_projections,
det.cam.trigger_mode,
"Overlapped",
)
# start the fly scan
yield from bps.trigger(det, group='fly')
yield from bps.abs_set(psofly.fly, "Fly", group='fly')
yield from bps.wait(group='fly')
# ------------------
# collect back white
# ------------------
# 1-7 move the sample out of the way
# NOTE:
# this will return ALL motors to starting positions, we need a
# smart way to calculate a shorter trajectory to move sample
# out of way
yield from bps.mv(preci, current_preci + dr)
yield from bps.mv(samx, current_samx + dx)
yield from bps.mv(samy, current_samy + dy)
# 1-7.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 2)
# 1-8 take the back white
yield from bps.mv(det.cam.num_images, n_frames * n_white)
yield from bps.trigger_and_read([det])
# 1-9 move sample back
yield from bps.mv(samx, current_samx)
yield from bps.mv(samy, current_samy)
yield from bps.mv(preci, current_preci)
# -----------------
# collect back dark
# -----------------
# 1-10 close the shutter
yield from bps.remove_suspender(suspend_A_shutter)
yield from bps.mv(A_shutter, "close")
# 1-10.5 set frame type for an organized HDF5 archive
yield from bps.mv(det.cam.frame_type, 3)
# 1-11 collect the back dark
yield from bps.mv(det.cam.num_images, n_frames * n_dark)
yield from bps.trigger_and_read([det])