class runnum(QThread):
"""Take ownership of the run number that is
synchronised between modules of PyDex.
By running this on a separated thread the
main GUI should not freeze up. PyQt signal/slot
architecture has a queue in the eventloop to
ensure function requests are not missed.
keyword arguments:
camra - an instance of ancam.cameraHandler.camera
saver - an instance of savim.imsaver.event_handler
saiaw - an instance of settingsgui.settings_window
check - an instance of atomChecker.atom_window
seq - an instance of sequencePreviewer.Previewer
n - the initial run ID number
m - the number of images taken per sequence
k - the number of images taken already"""
im_save = pyqtSignal(np.ndarray) # send an incoming image to saver
Dxstate = 'unknown' # current state of DExTer
def __init__(self, camra, saver, saiaw, check, seq, n=0, m=1, k=0):
super().__init__()
self._n = n # the run number
self._m = m # # images per run
self._k = k # # images received
self.multirun = False # status of whether in multirun or not
self.cam = camra # Andor camera control
self.cam.AcquireEnd.connect(
self.receive) # receive the most recent image
self.sv = saver # image saver
self.im_save.connect(
self.sv.add_item
) # separate signal to avoid risk of the slot being disconnected elsewhere
self.sv.start(
) # constantly checks queue, when an image to save is added to the queue, it saves it to a file.
self.sw = saiaw # image analysis settings gui
self.sw.m_changed.connect(self.set_m)
self.sw.CCD_stat_edit(self.cam.emg, self.cam.pag, self.cam.Nr,
True) # give image analysis the camera settings
self.cam.SettingsChanged.connect(self.sw.CCD_stat_edit)
self.cam.ROIChanged.connect(
self.sw.cam_pic_size_changed) # triggers pic_size_text_edit()
self.check = check # atom checker for ROIs, trigger experiment
self.check.rh.shape = (self.sw.stats['pic_width'],
self.sw.stats['pic_height'])
self.check.nrois_edit.setText(str(len(self.sw.stats['ROIs'])))
self.cam.ROIChanged.connect(self.check.rh.cam_pic_size_changed)
self.check.rh.resize_rois(self.sw.stats['ROIs'])
self.sw.bias_changed.connect(self.check.rh.set_bias)
self.check.roi_values.connect(self.sw.set_rois)
self.seq = seq # sequence editor
self.server = PyServer(
host='', port=8620) # server will run continuously on a thread
self.server.dxnum.connect(self.set_n) # signal gives run number
self.server.start()
if self.server.isRunning():
self.server.add_message(TCPENUM['TCP read'],
'Sync DExTer run number\n' + '0' * 2000)
self.trigger = PyServer(host='',
port=8621) # software trigger using TCP
self.trigger.start()
self.monitor = PyServer(host='',
port=8622) # monitor program runs separately
self.monitor.start()
self.monitor.add_message(self._n, 'resync run number')
def reset_server(self, force=False):
"""Check if the server is running. If it is, don't do anything, unless
force=True, then stop and restart the server. If the server isn't
running, then start it."""
for server in [self.server, self.trigger, self.monitor]:
if server.isRunning():
if force:
server.close()
server.clear_queue()
time.sleep(0.1) # give time for it to close
server.start()
else:
server.start()
def set_n(self, dxn):
"""Change the Dexter run number to the new value.
If it's during a multirun, check that the right number of
images were taken in the last run."""
self._n = int(dxn)
def set_m(self, newm):
"""Change the number of images per run"""
if newm > 0:
self._m = int(newm)
elif newm == 0:
self._m = 2
def receive(self, im=0):
"""Update the Dexter file number in all associated modules,
then send the image array to be saved and analysed."""
self.sv.dfn = str(self._n) # Dexter file number
imn = self._k % self._m # ID number of image in sequence
self.sv.imn = str(imn)
self.im_save.emit(im)
for i in self.sw.find(imn): # find the histograms that use this image
self.sw.mw[i].image_handler.fid = self._n
# (array, False if too many images were taken or if we're checking for atoms)
self.sw.mw[i].event_im.emit(
im, self._k < self._m and not self.check.checking)
self._k += 1 # another image was taken
def unsync_receive(self, im=0):
"""Receive an image array to be saved and analysed.
Count the number of images taken and use this to set the
DExTer file number in all associated modules."""
self.receive(im)
if self._k % self._m == 0:
self._k = 0
self.server.dxnum.emit(str(self._n + 1))
def mr_receive(self, im=0):
"""Receive an image as part of a multirun.
Update the Dexter file number in all associated modules,
then send the image array to be saved and analysed."""
self.sv.dfn = str(self._n) # Dexter file number
imn = self._k % self._m # ID number of image in sequence
self.sv.imn = str(imn)
self.im_save.emit(im)
if self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']
) >= self.seq.mr.mr_param['# omitted']:
for i in self.sw.find(imn):
self.sw.mw[i].image_handler.fid = self._n
self.sw.mw[i].event_im.emit(
im, self._k < self._m and not self.check.checking)
self._k += 1 # another image was taken
def check_receive(self, im=0):
"""Receive image for atom checker, don't save but just pass on"""
self.check.event_im.emit(im)
def reset_dates(self, t0):
"""Make sure that the dates in the image saving and analysis
programs are correct."""
date = time.strftime("%d %b %B %Y", t0).split(" ")
self.sv.reset_dates(self.sv.config_fn, date=date)
self.sw.reset_dates(date)
return ' '.join([date[0]] + date[2:])
#### atom checker ####
def atomcheck_go(self, toggle=True):
"""Disconnect camera images from analysis, start the camera
acquisition and redirect the images to the atom checker."""
if self.cam.initialised > 1:
self.check.checking = True
self.trigger.start(
) # start server for TCP to send msg when atoms loaded
# redirect images from analysis to atom checker
remove_slot(self.cam.AcquireEnd, self.receive, False)
remove_slot(self.cam.AcquireEnd, self.mr_receive, False)
remove_slot(self.cam.AcquireEnd, self.check_receive, True)
# still in external exposure trigger - DExTer will send the trigger pulses
self.cam.start() # run till abort keeps taking images
if self.check.timer.t0 > 0: # if timeout is set, set a timer
self.check.timer.singleShot(self.check.timer.t0 * 1e3,
self.check.send_trigger)
#### multirun ####
def multirun_go(self, toggle, stillrunning=False):
"""Initiate the multi-run: omit N files, save a histogram of M files, and
repeat for the user variables in the list. A new sequence is generated for
each multirun run. These are sent via TCP and then run. Once the multirun
has started it"""
r = self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']
) # ID of run in repetition cycle
if toggle: # and self.sw.check_reset() < now will auto reset (so you can queue up multiruns)
try: # take the multirun parameters from the queue (they're added to the queue in master.py)
self.seq.mr.mr_param, self.seq.mr.mrtr, self.seq.mr.mr_vals, appending = self.seq.mr.mr_queue.pop(
0) # parameters, sequence, values, whether to append
except IndexError as e:
logger.error(
'runid.py could not start multirun because no multirun was queued.\n'
+ str(e))
return 0
results_path = os.path.join(self.sv.results_path,
self.seq.mr.mr_param['measure_prefix'])
remove_slot(self.cam.AcquireEnd, self.receive,
False) # only receive if not in '# omit'
remove_slot(self.cam.AcquireEnd, self.mr_receive, True)
self.seq.mr.ind = 0 # counter for how far through the multirun we are
self._k = 0 # reset image per run count
try:
uv = self.seq.mr.mr_vals[0][0]
except IndexError:
uv = 'IndexError'
self.seq.mr.progress.emit( # update progress label
'multirun measure %s: %s: %s, omit %s of %s files, %s of %s histogram files, 0%% complete'
% (self.seq.mr.mr_param['measure'],
self.seq.mr.mr_param['Variable label'], uv, 0,
self.seq.mr.mr_param['# omitted'], 0,
self.seq.mr.mr_param['# in hist']))
# make the directories
os.makedirs(results_path, exist_ok=True)
os.makedirs(os.path.join(results_path, 'sequences'), exist_ok=True)
# save sequences and make list of messages to send and the order:
self.seq.mr.mrtr.write_to_file(
os.path.join(
results_path, 'sequences',
self.seq.mr.mr_param['measure_prefix'] + '_base.xml'))
self.seq.mr.get_all_sequences(
save_dir=os.path.join(results_path, 'sequences'))
self.seq.mr.save_mr_params(
os.path.join(
results_path,
self.seq.mr.mr_param['measure_prefix'] + 'params' +
str(self.seq.mr.mr_param['1st hist ID']) + '.csv'))
self.sw.init_analysers_multirun(
results_path, str(self.seq.mr.mr_param['measure_prefix']),
appending)
# tell the monitor program to save results to the new directory
self.monitor.add_message(self._n, results_path + '=save_dir')
self.monitor.add_message(self._n, 'start')
# insert TCP messages at the front of the queue: once the multirun starts don't interrupt it.
repeats = self.seq.mr.mr_param['# omitted'] + self.seq.mr.mr_param[
'# in hist']
mr_queue = [] # list of TCP messages for the whole multirun
for v in range(len(self.seq.mr.mr_vals)
): # use different last time step during multirun
mr_queue += [[
TCPENUM['TCP load last time step'],
self.seq.mr.mr_param['Last time step run'] + '0' * 2000
],
[
TCPENUM['TCP load sequence from string'],
self.seq.mr.msglist[v]
]] + [[
TCPENUM['Run sequence'], 'multirun run ' +
str(self._n + r + repeats * v) + '\n' +
'0' * 2000
] for r in range(repeats)] + [[
TCPENUM['TCP read'],
'save and reset histogram\n' + '0' * 2000
]]
# reset last time step for the last run:
mr_queue.insert(
len(mr_queue) - 2, [
TCPENUM['TCP load last time step'],
self.seq.mr.mr_param['Last time step end'] + '0' * 2000
])
mr_queue += [[
TCPENUM['TCP read'], 'confirm last multirun run\n' + '0' * 2000
],
[
TCPENUM['TCP read'], 'end multirun ' +
str(self.seq.mr.mr_param['measure']) + '\n' +
'0' * 2000
]]
for enum, text in mr_queue:
self.server.add_message(enum, text)
self.seq.mr.mr_param['runs included'][0].append(
self._n) # keep track of which runs are in the multirun.
else: # pause the multi-run
remove_slot(self.cam.AcquireEnd, self.mr_receive, False)
remove_slot(self.cam.AcquireEnd, self.receive,
True) # process every image
self.server.clear_queue()
self.cam.AF.AbortAcquisition()
self.multirun = stillrunning
if not stillrunning:
self.seq.mr.ind = 0
self._k = 0
for mw in self.sw.mw + self.sw.rw:
mw.multirun = ''
status = ' paused.' if stillrunning else ' ended.'
text = 'STOPPED. Multirun measure %s: %s is' % (
self.seq.mr.mr_param['measure'],
self.seq.mr.mr_param['Variable label'])
self.seq.mr.progress.emit(text + status)
self.server.add_message(TCPENUM['TCP read'], text + status)
self.server.add_message(TCPENUM['TCP read'], text + status)
def multirun_resume(self, status):
"""Resume the multi-run where it was left off.
If the multirun is already running, do nothing."""
if 'paused' in status:
remove_slot(self.cam.AcquireEnd, self.receive,
False) # only receive if not in '# omit'
remove_slot(self.cam.AcquireEnd, self.mr_receive, True)
self._k = 0 # reset image per run count
repeats = self.seq.mr.mr_param['# omitted'] + self.seq.mr.mr_param[
'# in hist']
r = self.seq.mr.ind % repeats # repeat
v = self.seq.mr.ind // repeats # variable
nrows = len(self.seq.mr.mr_vals)
if v > nrows - 1: v = nrows - 1
# finish this histogram
mr_queue = [[
TCPENUM['TCP read'],
'restart measure %s' % (self.seq.mr.mr_param['measure']) +
'\n' + '0' * 2000
],
[
TCPENUM['TCP load last time step'],
self.seq.mr.mr_param['Last time step run'] +
'0' * 2000
],
[
TCPENUM['TCP load sequence from string'],
self.seq.mr.msglist[v]
]]
mr_queue += [[
TCPENUM['Run sequence'],
'multirun run ' + str(self._n + i) + '\n' + '0' * 2000
] for i in range(repeats - r + 1)] + [[
TCPENUM['TCP read'], 'save and reset histogram\n' + '0' * 2000
]]
for var in range(v + 1, nrows): # add the rest of the multirun
mr_queue += [[
TCPENUM['TCP load sequence from string'],
self.seq.mr.msglist[var]
]] + [[
TCPENUM['Run sequence'], 'multirun run ' +
str(self._n + r + repeats * var) + '\n' + '0' * 2000
] for r in range(repeats)] + [[
TCPENUM['TCP read'],
'save and reset histogram\n' + '0' * 2000
]]
mr_queue.insert(
len(mr_queue) - 2, [
TCPENUM['TCP load last time step'],
self.seq.mr.mr_param['Last time step end'] + '0' * 2000
])
mr_queue += [[
TCPENUM['TCP read'], 'confirm last multirun run\n' + '0' * 2000
],
[
TCPENUM['TCP read'], 'end multirun ' +
str(self.seq.mr.mr_param['measure']) + '\n' +
'0' * 2000
]]
self.server.priority_messages(mr_queue) # adds at front of queue
def multirun_step(self, msg):
"""Update the status label for the multirun
The data for the run is received and processed when the command for the
next run is being sent, so the histogram is saved, fitted, and reset
based on the run number +1."""
self.monitor.add_message(self._n, 'update run number')
if self._k != self._m:
logger.warning('Run %s took %s / %s images.' %
(self._n, self._k, self._m))
self._k = 0
r = self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']) # repeat
if r == 1:
self.monitor.add_message(
self._n, 'set fadelines'
) # keep the trace from the start of the histogram
v = self.seq.mr.get_next_index(self.seq.mr.ind) # variable
try:
if r >= self.seq.mr.mr_param['# omitted']:
self.seq.mr.mr_param['runs included'][v].append(
self._n) # include this run in the multirun
uv = self.seq.mr.mr_vals[v][0] # get user variable
except IndexError:
if v == len(self.seq.mr.mr_vals):
uv = self.seq.mr.mr_vals[v - 1][0] # get user variable
else:
uv = 'IndexError'
self.seq.mr.ind += 1
r = self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist'])
self.seq.mr.progress.emit( # update progress label
'multirun measure %s: %s: %s, omit %s of %s files, %s of %s histogram files, %.3g %% complete'
% (self.seq.mr.mr_param['measure'],
self.seq.mr.mr_param['Variable label'], uv,
r if r < self.seq.mr.mr_param['# omitted'] else
self.seq.mr.mr_param['# omitted'],
self.seq.mr.mr_param['# omitted'],
r - self.seq.mr.mr_param['# omitted']
if r > self.seq.mr.mr_param['# omitted'] else 0,
self.seq.mr.mr_param['# in hist'], self.seq.mr.ind /
(self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']) / len(self.seq.mr.mr_vals) *
100))
def multirun_save(self, msg):
"""end of histogram: fit, save, and reset --- check this doesn't miss an image if there's lag"""
v = self.seq.mr.ind // (
self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']) - 1 # previous variable
try:
prv = self.seq.mr.mr_vals[v][
0] # get user variable from the previous row
except AttributeError as e:
logger.error(
'Multirun step could not extract user variable from table at row %s.\n'
% v + str(e))
prv = ''
# fit and save data
self.sw.multirun_save(self.sv.results_path,
self.seq.mr.mr_param['measure_prefix'],
self._n, prv,
str(v + self.seq.mr.mr_param['1st hist ID']))
def multirun_end(self, msg):
"""At the end of the multirun, save the plot data and reset"""
self.monitor.add_message(self._n, 'DAQtrace.csv=trace_file')
self.monitor.add_message(
self._n,
'save trace') # get the monitor to save the last acquired trace
self.sw.end_multirun() # reconnect signals and display empty hist
self.monitor.add_message(
self._n, 'save graph') # get the monitor to save the graph
self.monitor.add_message(self._n, 'stop') # stop monitoring
self.multirun_go(False) # reconnect signals
self.seq.mr.ind = 0
# save over log file with the parameters used for this multirun (now including run numbers):
self.seq.mr.save_mr_params(
os.path.join(
self.sv.results_path,
os.path.join(
self.seq.mr.mr_param['measure_prefix'],
self.seq.mr.mr_param['measure_prefix'] + 'params' +
str(self.seq.mr.mr_param['1st hist ID']) + '.csv')))
self.seq.mr.progress.emit( # update progress label
'Finished measure %s: %s.' %
(self.seq.mr.mr_param['measure'],
self.seq.mr.mr_param['Variable label']))
self.multirun = False
class runnum(QThread):
"""Take ownership of the run number that is
synchronised between modules of PyDex.
By running this on a separated thread the
main GUI should not freeze up. PyQt signal/slot
architecture has a queue in the eventloop to
ensure function requests are not missed.
keyword arguments:
camra - an instance of ancam.cameraHandler.camera
saver - an instance of savim.imsaver.event_handler
saiaw - an instance of settingsgui.settings_window
check - an instance of atomChecker.atom_window
seq - an instance of sequencePreviewer.Previewer
n - the initial run ID number
m - the number of images taken per sequence
k - the number of images taken already"""
im_save = pyqtSignal(np.ndarray) # send an incoming image to saver
Dxstate = 'unknown' # current state of DExTer
def __init__(self, camra, saver, saiaw, check, seq, n=0, m=1, k=0):
super().__init__()
self._n = n # the run number
self._m = m # # images per run
self._k = k # # images received
self.next_mr = [] # queue of messages for the next multirun
self.rearranging = False # whether the first image is being used for rearrangement.
self.mr_paused = False # whether the current multirun has been paused
self.cam = camra # Andor camera control
self.cam.AcquireEnd.connect(
self.receive) # receive the most recent image
self.sv = saver # image saver
self.im_save.connect(
self.sv.add_item
) # separate signal to avoid risk of the slot being disconnected elsewhere
self.sv.start(
) # constantly checks queue, when an image to save is added to the queue, it saves it to a file.
self.sw = saiaw # image analysis settings gui
self.sw.m_changed.connect(self.set_m)
self.sw.CCD_stat_edit(self.cam.emg, self.cam.pag, self.cam.Nr,
True) # give image analysis the camera settings
self.sw.reset_analyses(
) # make sure the loaded config settings are applied
self.cam.SettingsChanged.connect(self.sw.CCD_stat_edit)
self.cam.ROIChanged.connect(
self.sw.cam_pic_size_changed) # triggers pic_size_text_edit()
self.check = check # atom checker for ROIs, trigger experiment
self.check.recv_rois_action.triggered.connect(
self.get_rois_from_analysis)
# self.get_rois_from_analysis()
for rh in self.check.rh.values():
self.cam.ROIChanged.connect(rh.cam_pic_size_changed)
self.sw.bias_changed.connect(rh.set_bias)
self.check.roi_values.connect(self.sw.set_rois)
self.seq = seq # sequence editor
self.server = PyServer(
host='', port=8620, name='DExTer',
verbosity=1) # server will run continuously on a thread
self.server.dxnum.connect(self.set_n) # signal gives run number
self.server.start()
if self.server.isRunning():
self.server.add_message(TCPENUM['TCP read'],
'Sync DExTer run number\n' + '0' * 2000)
self.trigger = PyServer(
host='', port=8621,
name='Dx SFTWR TRIGGER') # software trigger using TCP
self.trigger.start()
self.monitor = PyServer(host='', port=8622,
name='DAQ') # monitor program runs separately
self.monitor.start()
self.monitor.add_message(self._n, 'resync run number')
self.awgtcp1 = PyServer(host='', port=8623,
name='AWG1') # AWG program runs separately
self.awgtcp1.start()
self.ddstcp1 = PyServer(host='', port=8624,
name='DDS1') # DDS program runs separately
self.ddstcp1.start()
self.seqtcp = PyServer(
host='', port=8625, name='BareDExTer'
) # Sequence viewer in seperate instance of LabVIEW
self.seqtcp.start()
self.slmtcp = PyServer(host='', port=8627,
name='SLM') # SLM program runs separately
self.slmtcp.start()
self.client = PyClient(host='129.234.190.235',
port=8626,
name='AWG1 recv') # incoming from AWG
self.client.start()
self.client.textin.connect(
self.add_mr_msgs) # msg from AWG starts next multirun step
self.awgtcp2 = PyServer(host='', port=8628,
name='AWG2') # AWG program runs separately
self.awgtcp2.start()
self.clien2 = PyClient(host='129.234.190.233',
port=8629,
name='AWG2 recv') # incoming from AWG
self.clien2.start()
self.clien2.textin.connect(
self.add_mr_msgs) # msg from AWG starts next multirun step
self.ddstcp2 = PyServer(host='', port=8630,
name='DDS2') # DDS program runs separately
self.ddstcp2.start()
def reset_server(self, force=False):
"""Check if the server is running. If it is, don't do anything, unless
force=True, then stop and restart the server. If the server isn't
running, then start it."""
for server in [
self.server, self.trigger, self.monitor, self.awgtcp1,
self.ddstcp1, self.slmtcp, self.seqtcp, self.awgtcp2,
self.ddstcp2
]:
if server.isRunning():
if force:
server.close()
server.clear_queue()
time.sleep(0.1) # give time for it to close
server.start()
else:
server.start()
def set_n(self, dxn):
"""Change the Dexter run number to the new value.
If it's during a multirun, check that the right number of
images were taken in the last run."""
if self._k != self._m and self.seq.mr.ind > 1:
warning('Run %s took %s / %s images.' %
(self._n, self._k, self._m))
self._n = int(dxn)
self._k = 0 # reset image count --- each run should start with im0
def set_m(self, newm):
"""Change the number of images per run"""
if newm > 0:
self._m = int(newm)
elif newm == 0:
self._m = 2
if self.rearranging: self._m += 1
def receive(self, im=0):
"""Update the Dexter file number in all associated modules,
then send the image array to be saved and analysed."""
self.sv.dfn = str(self._n) # Dexter file number
imn = self._k % self._m # ID number of image in sequence
if self.rearranging:
imn -= 1 # for rearranging, the 1st image doesn't go to analysis
self.sv.imn = str(imn)
self.im_save.emit(im)
if imn < 0:
self.check.event_im.emit(im)
else:
for i in self.sw.find(
imn): # find the histograms that use this image
self.sw.mw[i].image_handler.fid = self._n
self.sw.mw[i].event_im.emit(
im, self._k < self._m and not self.check.checking)
self._k += 1 # another image was taken
def unsync_receive(self, im=0):
"""Receive an image array to be saved and analysed.
Count the number of images taken and use this to set the
DExTer file number in all associated modules."""
self.receive(im)
if self._k % self._m == 0:
self._k = 0
self.server.dxnum.emit(str(self._n + 1))
def mr_receive(self, im=0):
"""Receive an image as part of a multirun.
Update the Dexter file number in all associated modules,
then send the image array to be saved and analysed."""
self.sv.dfn = str(self._n) # Dexter file number
imn = self._k % self._m # ID number of image in sequence
if self.rearranging:
imn -= 1 # for rearranging, the 1st image doesn't go to analysis
self.sv.imn = str(imn)
self.im_save.emit(im)
if imn < 0:
self.check.event_im.emit(im)
else:
if self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']
) >= self.seq.mr.mr_param['# omitted']:
for i in self.sw.find(imn):
self.sw.mw[i].image_handler.fid = self._n
self.sw.mw[i].event_im.emit(
im, self._k < self._m and not self.check.checking)
self._k += 1 # another image was taken
def check_receive(self, im=0):
"""Receive image for atom checker, don't save but just pass on"""
self.check.event_im.emit(im)
def reset_dates(self, t0):
"""Make sure that the dates in the image saving and analysis
programs are correct."""
date = time.strftime("%d %b %B %Y", t0).split(" ")
self.sv.reset_dates(self.sv.config_fn, date=date)
self.sw.reset_dates(date)
return ' '.join([date[0]] + date[2:])
#### atom checker ####
def get_rois_from_analysis(self, atom='Cs'):
self.check.rh[atom].cam_pic_size_changed(self.sw.stats['pic_width'],
self.sw.stats['pic_height'])
self.check.rh[atom].resize_rois(self.sw.stats['ROIs'])
def send_rearr_msg(self, msg=''):
"""Send the command to the AWG for rearranging traps"""
self.awgtcp1.priority_messages([(self._n,
'rearrange=' + msg + '#' * 2000)])
def send_rearr2_msg(self, msg=''):
"""Send the command to the 2nd AWG for rearranging traps"""
self.awgtcp2.priority_messages([(self._n,
'rearrange=' + msg + '#' * 2000)])
def atomcheck_go(self, toggle=True):
"""Disconnect camera images from analysis, start the camera
acquisition and redirect the images to the atom checker."""
if self.cam.initialised > 1:
self.check.checking = True
self.trigger.start(
) # start server for TCP to send msg when atoms loaded
# redirect images from analysis to atom checker
reset_slot(self.cam.AcquireEnd, self.receive, False)
reset_slot(self.cam.AcquireEnd, self.mr_receive, False)
reset_slot(self.cam.AcquireEnd, self.check_receive, True)
# still in external exposure trigger - DExTer will send the trigger pulses
self.cam.start() # run till abort keeps taking images
if self.check.timer.t0 > 0: # if timeout is set, set a timer
self.check.timer.singleShot(int(self.check.timer.t0 * 1e3),
self.check.send_trigger)
#### multirun ####
def get_params(self, v, module='AWG1'):
"""Reformat the multirun paramaters into a string to be sent to the AWG, DDS, or SLM"""
msg = module + ' set_data=['
col = -1 # in case the for loop doesn't execute
for col in range(len(self.seq.mr.mr_param['Type'])):
if 'AWG1' in self.seq.mr.mr_param['Type'][col] and module == 'AWG1':
try: # argument: value
for n in self.seq.mr.mr_param['Time step name'][
col]: # index of chosen AWG channel, segment
for m in self.seq.mr.mr_param['Analogue channel'][col]:
msg += '[%s, %s, "%s", %s, %s],' % (
n % 2, n // 2, self.seq.mr.awg_args[m],
self.seq.mr.mr_vals[v][col],
self.seq.mr.mr_param['list index'][col])
except Exception as e:
error('Invalid AWG parameter at (%s, %s)\n' % (v, col) +
str(e))
elif 'AWG2' in self.seq.mr.mr_param['Type'][
col] and module == 'AWG2':
try: # argument: value
for n in self.seq.mr.mr_param['Time step name'][
col]: # index of chosen AWG channel, segment
for m in self.seq.mr.mr_param['Analogue channel'][col]:
msg += '[%s, %s, "%s", %s, %s],' % (
n % 2, n // 2, self.seq.mr.awg_args[m],
self.seq.mr.mr_vals[v][col],
self.seq.mr.mr_param['list index'][col])
except Exception as e:
error('Invalid AWG parameter at (%s, %s)\n' % (v, col) +
str(e))
elif 'DDS1' in self.seq.mr.mr_param['Type'][
col] and module == 'DDS1':
try: # argument: value
for n in self.seq.mr.mr_param['Time step name'][
col]: # index of chosen DDS COM port, profile
for m in self.seq.mr.mr_param['Analogue channel'][col]:
port = '"P%s"' % (n % 9) if (n %
9) < 8 else '"aux"'
msg += '["COM%s", ' % (
(n // 9) + 7
) + port + ', "%s", %s],' % ( # we use COM7 - COM11
self.seq.mr.dds_args[m],
self.seq.mr.mr_vals[v][col])
except Exception as e:
error('Invalid DDS parameter at (%s, %s)\n' % (v, col) +
str(e))
elif 'DDS2' in self.seq.mr.mr_param['Type'][
col] and module == 'DDS2':
try: # argument: value
for n in self.seq.mr.mr_param['Time step name'][
col]: # index of chosen DDS COM port, profile
for m in self.seq.mr.mr_param['Analogue channel'][col]:
profile = '"P%s"' % (n % 9) if (n %
9) < 8 else '"aux"'
msg += '["%s", ' % (
n // 9 + 1
) + profile + ', "%s", %s],' % ( # don't specify COM port
self.seq.mr.dds_args[m],
self.seq.mr.mr_vals[v][col])
except Exception as e:
error('Invalid DDS parameter at (%s, %s)\n' % (v, col) +
str(e))
elif 'SLM' in self.seq.mr.mr_param['Type'][col] and module == 'SLM':
try: # argument: value
for n in self.seq.mr.mr_param['Time step name'][
col]: # index of chosen SLM hologram
for m in self.seq.mr.mr_param['Analogue channel'][col]:
msg += '[%s,"%s",%s],' % (
n, # [holo index, parameter, value]
self.seq.mr.slm_args[m],
self.seq.mr.mr_vals[v][col])
except Exception as e:
error('Invalid SLM parameter at (%s, %s)\n' % (v, col) +
str(e))
if col > -1: msg = msg[:-1] + ']'
else: msg += ']'
return msg
def multirun_go(self, toggle, stillrunning=False):
"""Initiate the multi-run: omit N files, save a histogram of M files, and
repeat for the user variables in the list. A new sequence is generated for
each multirun run. These are sent via TCP and then run. Once the multirun
has started it"""
r = self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']
) # ID of run in repetition cycle
if toggle: # and self.sw.check_reset() < now will auto reset (so you can queue up multiruns)
try: # take the multirun parameters from the queue (they're added to the queue in master.py)
self.seq.mr.mr_param, self.seq.mr.mrtr, self.seq.mr.mr_vals, self.seq.mr.appending = self.seq.mr.mr_queue.pop(
0) # parameters, sequence, values, whether to append
except IndexError as e:
error(
'runid.py could not start multirun because no multirun was queued.\n'
+ str(e))
return 0
results_path = os.path.join(self.sv.results_path,
self.seq.mr.mr_param['measure_prefix'])
reset_slot(self.cam.AcquireEnd, self.receive,
False) # only receive if not in '# omit'
reset_slot(self.cam.AcquireEnd, self.mr_receive, True)
self.seq.mr.ind = 0 # counter for how far through the multirun we are
self._k = 0 # reset image per run count
try:
uv = self.seq.mr.mr_vals[0][0]
except IndexError:
uv = 'IndexError'
self.seq.mr.progress.emit( # update progress label
'multirun measure %s: %s: %s, omit %s of %s files, %s of %s histogram files, 0%% complete'
% (self.seq.mr.mr_param['measure'],
self.seq.mr.mr_param['Variable label'], uv, 0,
self.seq.mr.mr_param['# omitted'], 0,
self.seq.mr.mr_param['# in hist']))
# make the directories
try:
os.makedirs(results_path, exist_ok=True)
os.makedirs(os.path.join(results_path, 'sequences'),
exist_ok=True)
# save sequences and make list of messages to send and the order:
self.seq.mr.mrtr.write_to_file(
os.path.join(
results_path, 'sequences',
self.seq.mr.mr_param['measure_prefix'] + '_base.xml'))
self.seq.mr.get_all_sequences(
save_dir=os.path.join(results_path, 'sequences'))
self.seq.mr.save_mr_params(
os.path.join(
results_path,
self.seq.mr.mr_param['measure_prefix'] + 'params' +
str(self.seq.mr.mr_param['1st hist ID']) + '.csv'))
self.sw.init_analysers_multirun(
results_path, str(self.seq.mr.mr_param['measure_prefix']),
self.seq.mr.appending)
except FileNotFoundError as e:
error(
'Multirun could not start because of invalid directory %s\n'
% results_path + str(e))
return 0
# tell the monitor program to save results to the new directory
self.monitor.add_message(self._n, results_path + '=save_dir')
self.monitor.add_message(self._n, 'start')
# insert TCP messages at the front of the queue: once the multirun starts don't interrupt it.
repeats = self.seq.mr.mr_param['# omitted'] + self.seq.mr.mr_param[
'# in hist']
# list of TCP messages for the whole multirun
# save AWG, DDS, and SLM params
self.awgtcp1.priority_messages([[
self._n, 'save=' + os.path.join(
results_path, 'AWG1param' +
str(self.seq.mr.mr_param['1st hist ID']) + '.txt')
]])
self.awgtcp2.priority_messages([[
self._n, 'save=' + os.path.join(
results_path, 'AWG2param' +
str(self.seq.mr.mr_param['1st hist ID']) + '.txt')
]])
self.ddstcp1.priority_messages([[
self._n, 'save_all=' + os.path.join(
results_path, 'DDS1param' +
str(self.seq.mr.mr_param['1st hist ID']) + '.txt')
]])
self.ddstcp2.priority_messages([[
self._n, 'save_all=' + os.path.join(
results_path, 'DDS2param' +
str(self.seq.mr.mr_param['1st hist ID']) + '.txt')
]])
self.slmtcp.priority_messages([[
self._n, 'save_all=' + os.path.join(
results_path, 'SLMparam' +
str(self.seq.mr.mr_param['1st hist ID']) + '.txt')
]])
mr_queue = []
#print('make msg')
for v in range(len(self.seq.mr.mr_vals)
): # use different last time step during multirun
module_msgs = {
'AWG1': '',
'AWG2': '',
'DDS1': '',
'DDS2': '',
'SLM': ''
}
for key in module_msgs.keys():
if any(key in x for x in self.seq.mr.mr_param['Type']
): # send parameters by TCP
module_msgs[key] = self.get_params(v, key)
pausemsg = '0' * 2000
if module_msgs['AWG1']: pausemsg = 'pause for AWG1' + pausemsg
if module_msgs['AWG2']: pausemsg = 'pause for AWG2' + pausemsg
mr_queue += [
[
TCPENUM['TCP read'],
module_msgs['AWG1'] + '||||||||' + '0' * 2000
], # set AWG parameters
[
TCPENUM['TCP read'],
module_msgs['AWG2'] + '||||||||' + '0' * 2000
], # set AWG parameters
[
TCPENUM['TCP read'],
module_msgs['DDS1'] + '||||||||' + '0' * 2000
], # set DDS parameters
[
TCPENUM['TCP read'],
module_msgs['DDS2'] + '||||||||' + '0' * 2000
], # set DDS parameters
[
TCPENUM['TCP read'],
module_msgs['SLM'] + '||||||||' + '0' * 2000
], # set SLM parameters
[
TCPENUM['TCP load last time step'],
self.seq.mr.mr_param['Last time step run'] + '0' * 2000
],
[
TCPENUM['TCP load sequence from string'],
self.seq.mr.msglist[v]
],
[TCPENUM['TCP read'], pausemsg]
] + [[
TCPENUM['Run sequence'], 'multirun run ' +
str(self._n + r + repeats * v) + '\n' + '0' * 2000
] for r in range(repeats)] + [[
TCPENUM['TCP read'],
'save and reset histogram\n' + '0' * 2000
]]
# reset last time step for the last run:
mr_queue.insert(
len(mr_queue) - 2, [
TCPENUM['TCP load last time step'],
self.seq.mr.mr_param['Last time step end'] + '0' * 2000
])
mr_queue += [[
TCPENUM['TCP read'], 'confirm last multirun run\n' + '0' * 2000
],
[
TCPENUM['TCP read'], 'end multirun ' +
str(self.seq.mr.mr_param['measure']) + '\n' +
'0' * 2000
]]
self.next_mr = mr_queue
self.add_mr_msgs()
self.seq.mr.mr_param['runs included'][0].append(
self._n) # keep track of which runs are in the multirun.
else: # pause the multi-run
reset_slot(self.cam.AcquireEnd, self.mr_receive, False)
reset_slot(self.cam.AcquireEnd, self.receive,
True) # process every image
if stillrunning:
self.next_mr = self.server.get_queue(
) # save messages to reinsert when resume
self.server.clear_queue()
if any('AWG1' in x for x in self.seq.mr.mr_param['Type']):
self.awgtcp1.add_message(
self._n,
'AWG1 load=' + os.path.join(
self.sv.results_path, # reset AWG parameters
self.seq.mr.mr_param['measure_prefix'],
'AWG1param' +
str(self.seq.mr.mr_param['1st hist ID']) + '.txt'))
if any('AWG2' in x for x in self.seq.mr.mr_param['Type']):
self.awgtcp2.add_message(
self._n,
'AWG2 load=' + os.path.join(
self.sv.results_path, # reset AWG parameters
self.seq.mr.mr_param['measure_prefix'],
'AWG2param' +
str(self.seq.mr.mr_param['1st hist ID']) + '.txt'))
if any('SLM' in x for x in self.seq.mr.mr_param['Type']):
self.slmtcp.add_message(
self._n,
'load_all=' + os.path.join(
self.sv.results_path, # reset SLM parameters
self.seq.mr.mr_param['measure_prefix'],
'SLMparam' + str(self.seq.mr.mr_param['1st hist ID']) +
'.txt'))
self.cam.AF.AbortAcquisition()
self.seq.mr.multirun = stillrunning
if not stillrunning:
self.seq.mr.ind = 0
self._k = 0
for mw in self.sw.mw + self.sw.rw:
mw.multirun = ''
status = ' paused.' if stillrunning else ' ended.'
self.mr_paused = stillrunning
text = 'STOPPED. Multirun measure %s: %s is' % (
self.seq.mr.mr_param['measure'],
self.seq.mr.mr_param['Variable label'])
self.seq.mr.progress.emit(text + status)
self.server.add_message(
TCPENUM['Run sequence'], text +
status) # a final run, needed to trigger the AWG to start.
def add_mr_msgs(self):
"""Add the next set of multirun messages to the queue to send to DExTer.
Gets triggered by the AWG TCP client."""
if self.seq.mr.multirun:
self.server.unlockq()
for i in range(len(self.next_mr)):
enum, text = self.next_mr.pop(0)
if not 'pause for AWG' in text:
self.server.add_message(enum, text)
else:
self.seq.mr.progress.emit('Waiting for AWG...')
self.server.lockq()
break
def skip_mr_hist(self):
"""Remove the TCP messages for the current histogram so that MR skips it"""
try:
queue = self.server.get_queue()
self.server.clear_queue()
for i, item in enumerate(queue): # find the end of the histogram
if 'save and reset histogram' in item[1]:
break
self.next_mr = [[TCPENUM['TCP read'], '||||||||' + '0' * 2000]
] + queue[i + 1:]
self.sw.all_hists(action='Reset')
r = self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist'])
self.seq.mr.ind += self.seq.mr.mr_param[
'# omitted'] + self.seq.mr.mr_param['# in hist'] - r
self.add_mr_msgs()
except IndexError as e:
error('Failed to skip histogram. IndexError:\n' + str(e))
def multirun_resume(self, status):
"""Resume the multi-run where it was left off.
If the multirun is already running, do nothing."""
if self.mr_paused:
self.mr_paused = False
reset_slot(self.cam.AcquireEnd, self.receive,
False) # only receive if not in '# omit'
reset_slot(self.cam.AcquireEnd, self.mr_receive, True)
self._k = 0 # reset image per run count
self.add_mr_msgs() # the messages were already stored in next_mr
def multirun_step(self, msg):
"""Update the status label for the multirun
The data for the run is received and processed when the command for the
next run is being sent, so the histogram is saved, fitted, and reset
based on the run number +1."""
self.monitor.add_message(self._n, 'update run number')
r = self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']) # repeat
if r == 1:
self.monitor.add_message(
self._n, 'set fadelines'
) # keep the trace from the start of the histogram
v = self.seq.mr.get_next_index(self.seq.mr.ind) # variable
try:
# if r >= self.seq.mr.mr_param['# omitted']:
# self.seq.mr.mr_param['runs included'][v].append(self._n) # include this run in the multirun
uv = self.seq.mr.mr_vals[v][0] # get user variable
except IndexError:
if v == len(self.seq.mr.mr_vals):
uv = self.seq.mr.mr_vals[v - 1][0] # get user variable
else:
uv = 'IndexError'
self.seq.mr.ind += 1
r = self.seq.mr.ind % (self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist'])
self.seq.mr.progress.emit( # update progress label
'multirun measure %s: %s: %s, omit %s of %s files, %s of %s histogram files, %.3g %% complete'
% (self.seq.mr.mr_param['measure'],
self.seq.mr.mr_param['Variable label'], uv,
r if r < self.seq.mr.mr_param['# omitted'] else
self.seq.mr.mr_param['# omitted'],
self.seq.mr.mr_param['# omitted'],
r - self.seq.mr.mr_param['# omitted']
if r > self.seq.mr.mr_param['# omitted'] else 0,
self.seq.mr.mr_param['# in hist'], self.seq.mr.ind /
(self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']) / len(self.seq.mr.mr_vals) *
100))
def multirun_save(self, msg):
"""end of histogram: fit, save, and reset --- check this doesn't miss an image if there's lag"""
v = self.seq.mr.ind // (
self.seq.mr.mr_param['# omitted'] +
self.seq.mr.mr_param['# in hist']) - 1 # previous variable
try:
prv = self.seq.mr.mr_vals[v][
0] # get user variable from the previous row
except AttributeError as e:
error(
'Multirun step could not extract user variable from table at row %s.\n'
% v + str(e))
prv = ''
# fit and save data
self.sw.multirun_save(self.sv.results_path,
self.seq.mr.mr_param['measure_prefix'],
self._n, prv,
str(v + self.seq.mr.mr_param['1st hist ID']))
def multirun_end(self, msg):
"""At the end of the multirun, save the plot data and reset"""
self.monitor.add_message(self._n, 'DAQtrace.csv=trace_file')
self.monitor.add_message(
self._n,
'save trace') # get the monitor to save the last acquired trace
self.sw.end_multirun() # reconnect signals and display empty hist
self.monitor.add_message(
self._n, 'save graph') # get the monitor to save the graph
self.monitor.add_message(self._n, 'stop') # stop monitoring
self.multirun_go(False) # reconnect signals
self.seq.mr.ind = 0
# save over log file with the parameters used for this multirun (now including run numbers):
self.seq.mr.save_mr_params(
os.path.join(
self.sv.results_path,
os.path.join(
self.seq.mr.mr_param['measure_prefix'],
self.seq.mr.mr_param['measure_prefix'] + 'params' +
str(self.seq.mr.mr_param['1st hist ID']) + '.csv')))
self.seq.mr.progress.emit( # update progress label
'Finished measure %s: %s.' %
(self.seq.mr.mr_param['measure'],
self.seq.mr.mr_param['Variable label']))
self.seq.mr.multirun = False