def to_xdi(self, filename=None):
'''Write an XDI-style file with bin energy in the first column and the
waveform of each of the 4 channels in the other columns.
'''
dcm, BMMuser, ring = user_ns['dcm'], user_ns['BMMuser'], user_ns[
'ring']
column_list = ['MCA1', 'MCA2', 'MCA3', 'MCA4']
column_list = [
f'MCA{channel_number}' for channel_number in self.channel_numbers
]
m2state, m3state = mirror_state()
handle = open(filename, 'w')
handle.write('# XDI/1.0 BlueSky/%s\n' % bluesky_version)
#handle.write('# Scan.uid: %s\n' % dataframe['start']['uid'])
#handle.write('# Scan.transient_id: %d\n' % dataframe['start']['scan_id'])
handle.write(
'# Beamline.name: BMM (06BM) -- Beamline for Materials Measurement'
)
handle.write('# Beamline.xray_source: NSLS-II three-pole wiggler\n')
handle.write(
'# Beamline.collimation: paraboloid mirror, 5 nm Rh on 30 nm Pt\n')
handle.write('# Beamline.focusing: %s\n' % m2state)
handle.write('# Beamline.harmonic_rejection: %s\n' % m3state)
handle.write('# Beamline.energy: %.3f\n' % dcm.energy.position)
handle.write(
'# Detector.fluorescence: SII Vortex ME4 (4-element silicon drift)\n'
)
handle.write('# Scan.end_time: %s\n' % now())
handle.write('# Scan.dwell_time: %.2f\n' % self.cam.acquire_time.value)
handle.write('# Facility.name: NSLS-II\n')
handle.write('# Facility.current: %.1f mA\n' % ring.current.value)
handle.write('# Facility.mode: %s\n' % ring.mode.value)
handle.write('# Facility.cycle: %s\n' % BMMuser.cycle)
handle.write('# Facility.GUP: %d\n' % BMMuser.gup)
handle.write('# Facility.SAF: %d\n' % BMMuser.saf)
handle.write('# Column.1: energy (eV)\n')
for c, mca_number in enumerate(column_list):
handle.write(f'# Column.{c+2}: MCA{mca_number} (counts)\n')
handle.write(
'# ==========================================================\n')
handle.write('# energy ')
## data table
e = numpy.arange(0, len(
self.channels.channel01.mca.array_data.get())) * 10
mca_data_array_list = [
channel.mca.array_data.get()
for channel in self.iterate_channels()
]
a = numpy.vstack(mca_data_array_list)
b = pandas.DataFrame(a.transpose(), index=e, columns=column_list)
handle.write(b.to_csv(sep=' '))
handle.flush()
handle.close()
print(bold_msg('wrote XRF spectra to %s' % filename))
def to_xdi(self, filename=None):
'''Write an XDI-style file with bin energy in the first column and the
waveform of the measurement channel in the second column.
'''
dcm, BMMuser, ring = user_ns['dcm'], user_ns['BMMuser'], user_ns[
'ring']
column_list = ['MCA8']
#template = " %.3f %.6f %.6f %.6f %.6f\n"
m2state, m3state = mirror_state()
handle = open(filename, 'w')
handle.write('# XDI/1.0 BlueSky/%s\n' % bluesky_version)
#handle.write('# Scan.uid: %s\n' % dataframe['start']['uid'])
#handle.write('# Scan.transient_id: %d\n' % dataframe['start']['scan_id'])
handle.write(
'# Beamline.name: BMM (06BM) -- Beamline for Materials Measurement'
)
handle.write('# Beamline.xray_source: NSLS-II three-pole wiggler\n')
handle.write(
'# Beamline.collimation: paraboloid mirror, 5 nm Rh on 30 nm Pt\n')
handle.write('# Beamline.focusing: %s\n' % m2state)
handle.write('# Beamline.harmonic_rejection: %s\n' % m3state)
handle.write('# Beamline.energy: %.3f\n' % dcm.energy.position)
handle.write(
'# Detector.fluorescence: SII Vortex ME4 (4-element silicon drift)\n'
)
handle.write('# Scan.end_time: %s\n' % now())
handle.write('# Scan.dwell_time: %.2f\n' %
self.settings.acquire_time.value)
handle.write('# Facility.name: NSLS-II\n')
handle.write('# Facility.current: %.1f mA\n' % ring.current.value)
handle.write('# Facility.mode: %s\n' % ring.mode.value)
handle.write('# Facility.cycle: %s\n' % BMMuser.cycle)
handle.write('# Facility.GUP: %d\n' % BMMuser.gup)
handle.write('# Facility.SAF: %d\n' % BMMuser.saf)
handle.write('# Column.1: energy (eV)\n')
handle.write('# Column.2: MCA1 (counts)\n')
handle.write(
'# ==========================================================\n')
handle.write('# energy ')
## data table
e = numpy.arange(0, len(self.mca1.value)) * 10
a = numpy.vstack([
self.mca1.value, self.mca2.value, self.mca3.value, self.mca4.value
])
b = pd.DataFrame(a.transpose(), index=e, columns=column_list)
handle.write(b.to_csv(sep=' '))
handle.flush()
handle.close()
print(bold_msg('wrote XRF spectra to %s' % filename))
def xrd_webcam(filename=None, **kwargs):
XRDURL = 'http://xf06bm-cam6/axis-cgi/jpg/image.cgi'
CAM_PROXIES = {
"http": None,
"https": None,
}
if filename is None:
filename = os.environ['HOME'] + '/XRD_camera_' + now() + '.jpg'
r = requests.get(XRDURL, proxies=CAM_PROXIES)
Image.open(BytesIO(r.content)).save(filename, 'JPEG')
if 'annotation' in kwargs:
annotate_image(filename, kwargs['annotation'])
report('XRD webcam image written to %s' % filename)
def analog_camera(filename=None,
sample=None,
folder=os.environ['HOME'],
device='/dev/video0',
camera=0,
skip=30,
frames=5,
brightness=30,
x=320,
y=240,
linecolor='white',
nocrosshair=True,
quiet=False,
reset=False,
usbid='534d:0021',
title='NIST BMM (NSLS-II 06BM)',
timestamp='%Y-%m-%d %H:%M:%S'):
"""A function for interacting with fswebcam in a way that meets the
needs of 06BM.
Parameters
----------
folder : str
location to drop jpg image [$HOME]
device : str
char device of camera [/dev/video0] should be set to something in /dev/v4l/by-id/
camera : int
camera number[0]
skip : int
number of frames to skip waiting for camera to wake up [30]
frames : int
number of frames to accumulate in image [5]
brightness : int
brightness setting of camera as a percentage [30]
x : int
middle of image, in pixels, X-location of cross hair [320]
y : int
middle of image, in pixels, Y-location of cross hair [240]
linecolor : str
color of cross hair lines [white]
nocrosshair : bool
flag to suppress cross hair [True]
quiet : bool
flag to suppress screen messages [False]
usbid : str
vendor and product ID of camera of AV to USB device at 06BM [534d:0021]
title : str
title string for fswebcam banner [NIST BMM (NSLS-II 06BM)]
filename : str
output file name
"""
USBDEVFS_RESET = 21780
if reset is True:
if not quiet: print("resetting video device")
try:
lsusb_out = Popen("lsusb | grep -i %s" % usbid,
shell=True,
bufsize=64,
stdin=PIPE,
stdout=PIPE,
close_fds=True).stdout.read().strip().split()
bus = lsusb_out[1].decode('UTF-8')
device = lsusb_out[3][:-1].decode('UTF-8')
print("/dev/bus/usb/%s/%s" % (bus, device))
f = open("/dev/bus/usb/%s/%s" % (bus, device), 'w', os.O_WRONLY)
fcntl.ioctl(f, USBDEVFS_RESET, 0)
sleep(1)
except Exception as msg:
print("failed to reset device:", msg)
quiet = ''
if quiet: quiet = '-q '
if filename is None:
filename = folder + '/analog_camera_' + now() + '.jpg'
if sample is not None and sample != '':
title = title + ' - ' + sample
if user_ns['BMMuser'].host == 'xf06bm-ws1':
command = [
'fswebcam', quiet, '-i', f'{camera}', '-d', device, '-r',
f'{x}x{y}', '--title', title, '--timestamp', timestamp, '-S',
f'{skip}', '-F', f'{frames}', '--set', f'brightness={brightness}%',
filename
]
else:
command = [
'ssh', 'xf06bm@xf06bm-ws1',
f"fswebcam {quiet}-i {camera} -d {device} -r {x}x{y} --title '{title}' --timestamp '{timestamp}' -S {skip} -F {frames} --set brightness={brightness}% '{filename}'"
]
run(command)
#command = f"fswebcam {quiet}-i {camera} -d {device} -r {x}x{y} --title '{title}' --timestamp '{timestamp}' -S {skip} -F {frames} --set brightness={brightness}% '{filename}'"
#system(command)
#command = f"fswebcam {quiet}-i {camera} -d {device} -r {x}x{y} --title '{title}' --timestamp '{timestamp}' -S {skip} -F {frames} --set brightness={brightness}% '{filename}'"
#system(f'ssh xf06bm@xf06bm-ws1 "{command}"')
report('Analog camera image written to %s' % filename)
def _capture(self, status, i):
"This runs on a background thread."
try:
if not self._acquiring_lock.acquire(timeout=0):
raise RuntimeError("Cannot trigger, currently trigggering!")
filename = os.path.join(self._root, self._rel_path_template % i)
# Kick off requests, or subprocess, or whatever with the result
# that a file is saved at `filename`.
if self._SPEC == "BMM_XAS_WEBCAM" or self._SPEC == "BMM_XRD_WEBCAM":
CAM_PROXIES = {
"http": None,
"https": None,
}
r = requests.get(self._url, proxies=CAM_PROXIES)
im = Image.open(BytesIO(r.content))
im.save(filename, 'JPEG')
#print(f'w: {im.width} h: {im.height}')
self.image.shape = (im.height, im.width, 3)
annotation = 'NIST BMM (NSLS-II 06BM) ' + self._annotation_string + ' ' + now(
)
annotate_image(filename, annotation)
else:
analog_camera(device=self.device,
x=self.x,
y=self.y,
brightness=self.brightness,
filename=filename,
sample=self._annotation_string,
folder=self._root,
quiet=True)
self.image.shape = (self.y, self.x, 3)
self._annotation_string = ''
datum = self._datum_factory({"index": i})
self._asset_docs_cache.append(('datum', datum))
self.image.set(datum["datum_id"]).wait()
except Exception as exc:
status.set_exception(exc)
else:
status.set_finished()
finally:
self._acquiring_lock.release()
def energystep(filename = None,
start = None,
end = None,
nsteps = None,
delay = 5,
dosteps = True):
'''A simple energy scan, just step forward in energy and don't measure
anything. This is a quick hack for use with a crude resonant
reflectivity experiment with IBM folks.
filename: name of file, will be appended to DATA for the full path (required)
start: starting energy value (required)
end: ending energy value (required)
nsteps: number of energy steps (required)
delay: pause between energy steps, in seconds [5]
dosteps: False to see energy values printed to screen without moving mono [True]
Writes a data file with columns of energy readback, energy
requested, time of epoch, and ISO 8601 timestamp
Example:
energystep(filename='blahblah', start=18936, end=19036, nsteps=101)
'''
BMMuser, dcm = user_ns['BMMuser'], user_ns['dcm']
BMM_log_info("energystep(filename=%s, start=%.1f, end=%.1f, nsteps=%d, delay=%.1f, dosteps=%s)" % (filename, start, end, nsteps, delay, str(dosteps)))
datafile = BMMuser.DATA + filename
handle = open(datafile, 'w')
handle.write('# energy steps from %.1f to %.1f in %d steps\n' % (start, end, nsteps))
handle.write('#----------------------------------------------------\n')
handle.write('# energy requested epoch iso8601\n')
handle.flush()
if dosteps:
yield from mv(dcm.energy, start)
print(' %.1f %.1f %.6f %s' % (dcm.energy.readback.get(), start, time.time(), now()))
handle.write(' %.1f %.1f %.6f %s\n' % (dcm.energy.readback.get(), start, time.time(), now()))
handle.flush()
yield from sleep(delay)
energy = start
estep = (end-start) / nsteps
while energy <= end:
if dosteps:
yield from mvr(dcm.energy, estep)
print(' %.1f %.1f %.6f %s' % (dcm.energy.readback.get(), energy, time.time(), now()))
handle.write(' %.1f %.1f %.6f %s\n' % (dcm.energy.readback.get(), energy, time.time(), now()))
handle.flush()
energy = energy + estep
yield from sleep(delay)
handle.flush()
handle.close()
def analog_camera(filename=None,
sample=None,
folder=os.environ['HOME'],
device='/dev/video0',
camera=0,
skip=30,
frames=5,
brightness=20,
x=320,
y=240,
linecolor='white',
nocrosshair=True,
quiet=False,
reset=False,
usbid='534d:0021',
title='NIST BMM (NSLS-II 06BM)',
timestamp='%Y-%m-%d %H:%M:%S'):
"""A function for interacting with fswebcam in a way that meets the
needs of 06BM.
Parameters:
folder: location to drop jpg image [$HOME]
device: char device of camera [/dev/video0]
camera: camera number [0]
skip: number of frames to skip waiting for camera to wake up [30]
frames: number of frames to accumulate in image [5]
brightness: brightness setting of camera as a percentage [20]
x: X-location of cross hair [320] (middle of image)
y: Y-location of cross hair [240] (middle of image)
linecolor: color of cross hair lines [white]
nocrosshair: flag to suppress cross hair [True]
quiet: flag to suppress screen messages [False]
usbid: vendor and product ID of camera [534d:0021] (AV to USB device at 06BM)
title: title string for fswebcam banner [NIST BMM (NSLS-II 06BM)]
filename: output file name [ISO 8601 timestamp in folder]
"""
USBDEVFS_RESET = 21780
if reset is True:
if not quiet: print("resetting video device")
try:
lsusb_out = Popen("lsusb | grep -i %s" % usbid,
shell=True,
bufsize=64,
stdin=PIPE,
stdout=PIPE,
close_fds=True).stdout.read().strip().split()
bus = lsusb_out[1].decode('UTF-8')
device = lsusb_out[3][:-1].decode('UTF-8')
print("/dev/bus/usb/%s/%s" % (bus, device))
f = open("/dev/bus/usb/%s/%s" % (bus, device), 'w', os.O_WRONLY)
fcntl.ioctl(f, USBDEVFS_RESET, 0)
sleep(1)
except Exception as msg:
print("failed to reset device:", msg)
quiet = ''
if quiet: quiet = '-q '
if filename is None:
filename = folder + '/analog_camera_' + now() + '.jpg'
if sample is not None:
title = title + ' - ' + sample
command = "fswebcam %s-i %s -d %s -r 640x480 --title \"%s\" --timestamp \"%s\" -S %d -F %d --set brightness=%s%% \"%s\"" %\
(quiet, camera, device, title, timestamp, skip, frames, brightness, filename)
system(command)
report('Analog camera image written to %s' % filename)
def main_plan(detector, slow, startslow, stopslow, nslow, fast, startfast,
stopfast, nfast, pluck, force, dwell, md):
(ok, text) = BMM_clear_to_start()
if force is False and ok is False:
print(error_msg(text))
BMMuser.final_log_entry = False
yield from null()
return
user_ns['RE'].msg_hook = None
## sanity checks on slow axis
if type(slow) is str: slow = slow.lower()
if slow not in motor_nicknames.keys() and 'EpicsMotor' not in str(
type(slow)) and 'PseudoSingle' not in str(type(slow)):
print(
error_msg('\n*** %s is not an areascan motor (%s)\n' %
(slow, str.join(', ', motor_nicknames.keys()))))
BMMuser.final_log_entry = False
yield from null()
return
if slow in motor_nicknames.keys():
slow = motor_nicknames[slow]
## sanity checks on fast axis
if type(fast) is str: fast = fast.lower()
if fast not in motor_nicknames.keys() and 'EpicsMotor' not in str(
type(fast)) and 'PseudoSingle' not in str(type(fast)):
print(
error_msg('\n*** %s is not an areascan motor (%s)\n' %
(fast, str.join(', ', motor_nicknames.keys()))))
BMMuser.final_log_entry = False
yield from null()
return
if fast in motor_nicknames.keys():
fast = motor_nicknames[fast]
detector = detector.capitalize()
yield from mv(_locked_dwell_time, dwell)
dets = [
quadem1,
]
if with_xspress3 and detector == 'If':
detector = 'Xs'
if detector == 'If':
dets.append(vor)
detector = 'ROI1'
if detector.lower() == 'xs':
dets.append(xs)
detector = BMMuser.xs1
yield from mv(xs.total_points, nslow * nfast)
if 'PseudoSingle' in str(type(slow)):
valueslow = slow.readback.get()
else:
valueslow = slow.user_readback.get()
line1 = 'slow motor: %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(slow.name, startslow, stopslow, nslow, valueslow)
if 'PseudoSingle' in str(type(fast)):
valuefast = fast.readback.get()
else:
valuefast = fast.user_readback.get()
line2 = 'fast motor: %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(fast.name, startfast, stopfast, nfast, valuefast)
npoints = nfast * nslow
estimate = int(npoints * (dwell + 0.7))
# extent = (
# valuefast + startfast,
# valueslow + startslow,
# valuefast + stopfast,
# valueslow + stopslow,
# )
# extent = (
# 0,
# nfast-1,
# 0,
# nslow-1
# )
# print(extent)
# return(yield from null())
# areaplot = LiveScatter(fast.name, slow.name, detector,
# xlim=(startfast, stopfast), ylim=(startslow, stopslow))
close_all_plots()
areaplot = LiveGrid(
(nslow, nfast),
detector, #aspect='equal', #aspect=float(nslow/nfast), extent=extent,
xlabel='fast motor: %s' % fast.name,
ylabel='slow motor: %s' % slow.name)
#BMMuser.ax = areaplot.ax
#BMMuser.fig = areaplot.ax.figure
BMMuser.motor = fast
BMMuser.motor2 = slow
#BMMuser.fig.canvas.mpl_connect('close_event', handle_close)
thismd = dict()
thismd['XDI'] = dict()
thismd['XDI']['Facility'] = dict()
thismd['XDI']['Facility']['GUP'] = BMMuser.gup
thismd['XDI']['Facility']['SAF'] = BMMuser.saf
thismd['slow_motor'] = slow.name
thismd['fast_motor'] = fast.name
report(
f'Starting areascan at x,y = {fast.position:.3f}, {slow.position:.3f}',
level='bold',
slack=True)
## engage suspenders right before starting scan sequence
if force is False: BMM_suspenders()
@subs_decorator(areaplot)
#@subs_decorator(src.callback)
def make_areascan(dets,
slow,
startslow,
stopslow,
nslow,
fast,
startfast,
stopfast,
nfast,
snake=False):
BMMuser.final_log_entry = False
uid = yield from grid_scan(
dets,
slow,
startslow,
stopslow,
nslow,
fast,
startfast,
stopfast,
nfast,
snake,
md={
'plan_name':
f'grid_scan measurement {slow.name} {fast.name} {detector}'
})
BMMuser.final_log_entry = True
return uid
rkvs.set('BMM:scan:type', 'area')
rkvs.set('BMM:scan:starttime',
str(datetime.datetime.timestamp(datetime.datetime.now())))
rkvs.set('BMM:scan:estimated', estimate)
BMM_log_info('begin areascan observing: %s\n%s%s' %
(detector, line1, line2))
uid = yield from make_areascan(dets,
slow,
valueslow + startslow,
valueslow + stopslow,
nslow,
fast,
valuefast + startfast,
valuefast + stopfast,
nfast,
snake=False)
if pluck is True:
close_all_plots()
thismap = user_ns['db'].v2[uid]
x = numpy.array(thismap.primary.read()[fast.name])
y = numpy.array(thismap.primary.read()[slow.name])
z=numpy.array(thismap.primary.read()[BMMuser.xs1]) +\
numpy.array(thismap.primary.read()[BMMuser.xs2]) +\
numpy.array(thismap.primary.read()[BMMuser.xs3]) +\
numpy.array(thismap.primary.read()[BMMuser.xs4])
z = z.reshape(nfast, nslow)
# grabbing the first nfast elements of x and every
# nslow-th element of y is more reliable than
# numpy.unique due to float &/or motor precision issues
#plt.title(f'Energy = {energies["below"]}')
plt.xlabel(f'fast axis ({fast.name}) position (mm)')
plt.ylabel(f'slow axis ({slow.name}) position (mm)')
plt.gca().invert_yaxis() # plot an xafs_x/xafs_y plot upright
plt.contourf(x[:nfast], y[::nslow], z, cmap=plt.cm.viridis)
plt.colorbar()
plt.show()
fname = os.path.join(BMMuser.folder, 'map-' + now() + '.png')
plt.savefig(fname)
try:
img_to_slack(fname)
except:
post_to_slack('failed to post image: {fname}')
pass
BMMuser.x = None
figs = list(map(plt.figure, plt.get_fignums()))
canvas = figs[0].canvas
action = input('\n' + bold_msg(
'Pluck motor position from the plot? [Y/n then Enter] '))
if action.lower() == 'n' or action.lower() == 'q':
return (yield from null())
print(
'Single click the left mouse button on the plot to pluck a point...'
)
cid = canvas.mpl_connect(
'button_press_event',
interpret_click) # see 65-derivedplot.py and
while BMMuser.x is None: # https://matplotlib.org/users/event_handling.html
yield from sleep(0.5)
# print('Converting plot coordinates to real coordinates...')
# begin = valuefast + startfast
# stepsize = (stopfast - startfast) / (nfast - 1)
# pointfast = begin + stepsize * BMMuser.x
# #print(BMMuser.x, pointfast)
# begin = valueslow + startslow
# stepsize = (stopslow - startslow) / (nslow - 1)
# pointslow = begin + stepsize * BMMuser.y
# #print(BMMuser.y, pointslow)
# print('That translates to x=%.3f, y=%.3f' % (pointfast, pointslow))
yield from mv(fast, BMMuser.x, slow, BMMuser.y)
report(
f'Moved to position x,y = {fast.position:.3f}, {slow.position:.3f}',
level='bold',
slack=True)
