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running changes made by M.Appleby and J.Beale. Mainly to update due to python 3.10

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This commit is contained in:
John Henry Beale
2025-11-10 10:47:31 +01:00
parent 84d74d5d23
commit c4c5ea6491
4 changed files with 182 additions and 96 deletions
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236
psi_device.py
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@@ -3,22 +3,23 @@ import logging,sys,os,socket
from math import ceil
_log=logging.getLogger(__name__)
if __name__ == "__main__":
logging.basicConfig(level=logging.DEBUG,format='%(name)s:%(levelname)s:%(module)s:%(lineno)d:%(funcName)s:%(message)s ')
logging.getLogger('matplotlib').setLevel(logging.INFO)
logging.basicConfig(level=logging.DEBUG,format='%(name)s:%(levelname)s:%(module)s:%(lineno)d:%(funcName)s:%(message)s ')
logging.getLogger('matplotlib').setLevel(logging.INFO)
if socket.gethostname()=='ganymede':
base=os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.abspath(os.path.join(base,'../PBSwissMX/python')))
sys.path.insert(0, os.path.abspath(os.path.join(base,'../../PBTools')))
else:
base=os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.join(base,'PBTools'))
sys.path.insert(0, os.path.join(base,'PBSwissMX/python'))
elif socket.gethostname()!='ganymede':
print('past logging')
if socket.gethostname()=='ganymede':
base=os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.abspath(os.path.join(base,'../PBSwissMX/python')))
sys.path.insert(0, os.path.abspath(os.path.join(base,'../../PBTools')))
else:
base=os.path.abspath(os.path.dirname(__file__))
sys.path.insert(0, os.path.join(base,'PBTools'))
sys.path.insert(0, os.path.join(base,'PBSwissMX/python'))
sys.path.insert(0, os.path.expanduser('/sf/cristallina/applications/slic/slic-package'))
sys.path.insert(0, os.path.expanduser('/sf/cristallina/applications/mx/swissmx_tools/jfj'))
from PyQt5.QtWidgets import (QApplication,)
from app_config import AppCfg #settings, option, toggle_option
@@ -34,6 +35,7 @@ try:
from ctadaq import CTAAcquisition
from jfjoch_device import JFJ
except ImportError as e:
print(f"error {e}")
_log.warning(e)
@@ -125,6 +127,9 @@ class Jungfrau:
_log.critical(f'Jungfrau not connected: {e}')
self.n_pulses_run = None
self.bsdata_scalar = 1
self.motion_mode = None
self.block_size_to_jungfrau = 1000
self.block_size_to_slic = 1000
def config(self,**kwargs):
if getattr(self,'_sim',False):
@@ -133,7 +138,7 @@ class Jungfrau:
app=QApplication.instance() #temproary fix, couldnt access these in function, maybe the bt above needs to be self.detectors ... etc
cfg=app._cfg
det = cfg.value(AppCfg.DAQ_DET)
print("det", repr(det))
#print("det", repr(det))
detectors = [det] if det.get("name") else None
bs_channels = cfg.value(AppCfg.DAQ_BS_CH)
pv_channels = cfg.value(AppCfg.DAQ_PV_CH)
@@ -144,6 +149,9 @@ class Jungfrau:
sync_mode=dt_misc['sync_mode']
sync_flag=dt_misc['sync_flag']
self.n_pulses_run = None
#print(kwargs)
motion_mode = kwargs['mode']
self.motion_mode = motion_mode
if loc['jungfraujoch']:
try:
#self.jfj = JFJ("http://sf-daq-2:5232") old port
@@ -159,70 +167,130 @@ class Jungfrau:
self.jfj = None
_log.info(f'JungFrauJoch is not in use')
print('JungFrauJoch not in use')
if sync_flag==0:
#if sync_flag==0:
if motion_mode == 1 or motion_mode == 3:
#grid_cnt=kwargs['grid']['count']
repetitions=int(kwargs['points'][:, 0].max())+1 #grid_cnt[0] #'x' or number of columns # if mode = 1 or 3
cta_multiplier=int(kwargs['points'][:, 1].max())+1#grid_cnt[1] #'y' or number of appertures in a column/number of rows
elif motion_mode == 4 or motion_mode == 5 or motion_mode == 6:
grid_cnt=kwargs['grid']['count']
repetitions=grid_cnt[0] #'x' or number of columns
repetitions=grid_cnt[0] #'x' or number of columns # if mode = 1 or 3
cta_multiplier=grid_cnt[1] #'y' or number of appertures in a column/number of rows
number_of_appertures = repetitions*cta_multiplier
cta=CTASequencer("SAR-CCTA-ESC")
cta.cfg.repetitions = repetitions
self.images=repetitions*cta_multiplier
if code_gen==3:
if kwargs['tmove']==0:
wait_pulses=0
else:
wait_pulses=kwargs['twait']//kwargs['tmove']
#xray_seq=[0,]*wait_pulses+[1] # multiplier is proportional to wait_time i.e. 10 ms = 1, 20 ms =2, 30 ms =3.
#xray_sequence=[0,]*wait_pulses+[1]
#cta.seq[200]=xray_sequence*cta_multiplier # x-ray_shutter
#cta.seq[214] = [1,] + [0,] * (len(xray_sequence * cta_multiplier) -1)
#trigger_sequence = [1,] + [0,] * wait_pulses + [0,] * wait_pulses + [0]
#cta.seq[215]=trigger_sequence*(cta_multiplier//2) # laser_shutter
#image_label_sequence = [0,] * wait_pulses + [1] + [0,] * wait_pulses + [0]
#cta.seq[216]=image_label_sequence*(cta_multiplier//2)
#cta.seq[219] = xray_sequence * cta_multiplier
on_off_ratio = 2 #1 on to 1 off which means 2 in the whole sequence
xray_sequence = [0,] * (wait_pulses - 1) + [1,] + [0,]
cta.seq[200] = xray_sequence * cta_multiplier # x-ray_shutter
cta.seq[214] = [1,] + [0,] * (len(xray_sequence * cta_multiplier) -1) #start motion
if run["triggered"]:
trigger_on = [0,] * wait_pulses + [1,]
trigger_off = [0,] + [0,] * wait_pulses
trigger_sequence = trigger_on * (on_off_ratio-1) + trigger_off
image_on = [0,] * (wait_pulses - 1) + [1,] + [0,]
image_label_sequence = [0,] +[0,] * wait_pulses + image_on * (on_off_ratio-1)
cta.seq[215] = trigger_sequence * (cta_multiplier//on_off_ratio) # trigger (laser_shutter or droplet ejector)
cta.seq[216] = image_label_sequence * (cta_multiplier//on_off_ratio) # image label (on or off)
else:
no_trigger_sequence = [0,] * (wait_pulses - 1) + [0,] + [0,]
cta.seq[215] = no_trigger_sequence * cta_multiplier # x-ray_shutter # trigger (laser_shutter or droplet ejector)
cta.seq[216] = no_trigger_sequence * cta_multiplier # x-ray_shutter # image label (on or off)1
cta.seq[219] = xray_sequence * cta_multiplier # detector trigger
number_of_appertures = repetitions*cta_multiplier
cta=CTASequencer("SAR-CCTA-ESC")
cta.cfg.repetitions = repetitions
self.images=repetitions*cta_multiplier
on_off_ratio = int(run['num_of_on_to_1_off'])+1
if motion_mode==5:
if kwargs['tmove']==0:
wait_pulses=0
else:
print('not code gen 3')
# no extra rows 1:1
cta.seq[214]=[1,]+[0,]*(cta_multiplier-1) #start motion
cta.seq[200]=[1,]*cta_multiplier #uncomment me for normal operation
#cta.seq[200]=[1,0,]*(cta_multiplier//2) # x-ray_shutter
cta.seq[219]=[1,]*cta_multiplier #trigger detector
if run["triggered"]:
cta.seq[215]=[1,0,]*(cta_multiplier//2) # Trigger 1:1
cta.seq[216]=[1,0,]*(cta_multiplier//2) # Label image light dark 1:1 #change back to 1,0 for normal on off measurements
wait_pulses=kwargs['twait']//kwargs['tmove']
#xray_seq=[0,]*wait_pulses+[1] # multiplier is proportional to wait_time i.e. 10 ms = 1, 20 ms =2, 30 ms =3.
#xray_sequence=[0,]*wait_pulses+[1]
#cta.seq[200]=xray_sequence*cta_multiplier # x-ray_shutter
#cta.seq[214] = [1,] + [0,] * (len(xray_sequence * cta_multiplier) -1)
#trigger_sequence = [1,] + [0,] * wait_pulses + [0,] * wait_pulses + [0]
#cta.seq[215]=trigger_sequence*(cta_multiplier//2) # laser_shutter
#image_label_sequence = [0,] * wait_pulses + [1] + [0,] * wait_pulses + [0]
#cta.seq[216]=image_label_sequence*(cta_multiplier//2)
#cta.seq[219] = xray_sequence * cta_multiplier
#on_off_ratio = 2 #1 on to 1 off which means 2 in the whole sequence
xray_sequence = [0,] * wait_pulses + [1,]
cta.seq[200] = xray_sequence * cta_multiplier # x-ray_shutter
cta.seq[214] = [1,] + [0,] * (len(xray_sequence * cta_multiplier) -1) #start motion
if run["triggered"]:
trigger_on = [1,] + [0,] * wait_pulses
trigger_off = [0,] + [0,] * wait_pulses
trigger_sequence = trigger_off + trigger_on * (on_off_ratio-1)
image_on = [0,] * wait_pulses + [1,]
image_label_sequence = [0,] * wait_pulses + [0,] + image_on * (on_off_ratio-1)
cta.seq[215] = trigger_sequence * int(cta_multiplier/on_off_ratio) # trigger (laser_shutter or droplet ejector)
cta.seq[216] = image_label_sequence * int(cta_multiplier/on_off_ratio) # image label (on or off)
else:
no_trigger_sequence = [0,] + [0,] * wait_pulses
cta.seq[215] = no_trigger_sequence * cta_multiplier # x-ray_shutter # trigger (laser_shutter or droplet ejector)
cta.seq[216] = no_trigger_sequence * cta_multiplier # x-ray_shutter # image label (on or off)1
cta.seq[219] = xray_sequence * cta_multiplier # detector trigger
self.n_pulses_run = len(cta.seq[200])*repetitions
self.bsdata_scalar = self.n_pulses_run/number_of_appertures
_log.info(f'The multiplier of the block size is {self.bsdata_scalar}')
cta.seq.upload()
self._daq=CTAAcquisition(cta, loc['end_station'], loc['p_group'], default_detectors=detectors,
default_channels=bs_channels,
default_pvs=pv_channels, rate_multiplicator=1, append_user_tag_to_data_dir=True, timeout=30)
#print(on_off_ratio,cta_multiplier,int(cta_multiplier/on_off_ratio),len(cta.seq[200]),len(cta.seq[214]),len(cta.seq[215]),len(cta.seq[216]),len(cta.seq[219]))
#self.motion_mode = 5
elif motion_mode==6:
ssz = kwargs['ssz']
#smv = kwargs['smv']
grid_cnt=kwargs['grid']['count']
repetitions=grid_cnt[0] #'x' or number of columns # if mode = 1 or 3
cta_multiplier=grid_cnt[1] #'y' or number of appertures in a column/number of rows
smv = ssz[0]-1 #max(ssz[0]-1, ssz[1]) commented out for fast camera tests, need a better work around for non-equal jumps in the CTA or motion script, currently avoid!
apperture_group_size = ssz[0] * ssz[1]
#number_of_apperture_groups = number_of_appertures // apperture_group_size
number_of_apperture_groups=(repetitions//ssz[0])*(cta_multiplier//ssz[1])
print(f"number_of_apperture_groups = {number_of_apperture_groups}")
#print(f"actually want 162//8 * {162//7} (or 162//8 * 162//7) which = 460, so 460*8*7=25760")
transition_pulses = smv
#on_off_ratio = 2 #1 on to 1 off which means 2 in the whole sequence
xray_sequence = [0,] * apperture_group_size + [1,] * apperture_group_size + [0,] * (transition_pulses - 1)
cta.seq[200] = xray_sequence
cta.seq[214] = [1,] + [0,] * (apperture_group_size -1) + [0,] * apperture_group_size + [0,] * (transition_pulses - 1) #start motion
if run["triggered"]:
if on_off_ratio > apperture_group_size:
on_off_ratio = apperture_group_size
on_off_sequence = [1,] * (on_off_ratio - 1) + [0,]
cta.seq[215] = on_off_sequence * (apperture_group_size//on_off_ratio) + [0,] * apperture_group_size + [0,] * (transition_pulses -1) # Trigger 1:1
repeat_sequence_laser_closed = [1, ] + [0,] * (apperture_group_size - 1)
repeat_sequence_laser_open = [1,] + [0,] * (apperture_group_size - 1)
tranisition_sequence_laser_shut = [0,] * (transition_pulses - 1) #close shutter after final point before starting move...?
cta.seq[213] = repeat_sequence_laser_open + repeat_sequence_laser_closed + tranisition_sequence_laser_shut # Trigger 1:1
cta.seq[216] = [0,] * apperture_group_size + on_off_sequence * (apperture_group_size//on_off_ratio) + [0,] * (transition_pulses - 1) # Label image light dark 1:1 #change back to 1,0 for normal on off measurements
else:
cta.seq[215] = [0] * apperture_group_size * 2 + [0,] * (transition_pulses - 1) # trigger (laser_shutter or droplet ejector)
cta.seq[216] = [0] * apperture_group_size * 2 + [0,] * (transition_pulses -1) # image label (on or off)1
cta.seq[219] = xray_sequence # detector trigger
self.n_pulses_run = len(cta.seq[200])*number_of_apperture_groups
cta.cfg.repetitions = number_of_apperture_groups # number of repeitions is now number of times we repeat the loop
self.images=number_of_apperture_groups*apperture_group_size
#self.bsdata_scalar = self.n_pulses_run/number_of_appertures
data_collection_block_scaler = round(1000/apperture_group_size)
self.block_size_to_jungfrau = data_collection_block_scaler*apperture_group_size
self.block_size_to_slic = data_collection_block_scaler*len(cta.seq[200])
print(f"length of sequence = {len(cta.seq[200])}")
print(f"apperture in group = {apperture_group_size}")
print(f"number_of_apperture_groups = {number_of_apperture_groups}")
#print(f"n_pulses = {self.n_pulses_run} and n_appertures and images = {number_of_appertures}")
#print(f"so a scalar of {self.bsdata_scalar}")
print(f"using a data_collection_block_scaler of {data_collection_block_scaler}")
print(f"block_size for slic {self.block_size_to_slic}")
print(f"block size for jungfrau {self.block_size_to_jungfrau}")
else:
self._daq=SFAcquisition(
loc['end_station'], loc['p_group'],
default_detectors=detectors, default_channels=bs_channels, default_pvs=pv_channels,
rate_multiplicator=1, append_user_tag_to_data_dir=True)
_log.info('not mode 5 or 6')
#need to add on off ratio
# no extra rows 1:1
#self.motion_mode = 4
cta.seq[214]=[1,]+[0,]*(cta_multiplier-1) #start motion
cta.seq[200]=[1,]*cta_multiplier #uncomment me for normal operation
#cta.seq[200]=[1,0,]*(cta_multiplier//2) # x-ray_shutter
cta.seq[219]=[1,]*cta_multiplier #trigger detector
if run["triggered"]:
#cta.seq[215]=[1,0,]*(cta_multiplier//2) # Trigger 1:1
cta.seq[215]=[1,]*cta_multiplier # shutter always open
cta.seq[216]=[1,0,]*(cta_multiplier//2) # Label image light dark 1:1 #change back to 1,0 for normal on off measurements
self.n_pulses_run = len(cta.seq[200])*repetitions
self.bsdata_scalar=1
cta.seq.upload()
self._daq=CTAAcquisition(cta, loc['end_station'], loc['p_group'], default_detectors=detectors,
default_channels=bs_channels,
default_pvs=pv_channels, rate_multiplicator=1, append_user_tag_to_data_dir=True)#, timeout=30)
#else:
# self._daq=SFAcquisition(
# loc['end_station'], loc['p_group'],
# default_detectors=detectors, default_channels=bs_channels, default_pvs=pv_channels,
# rate_multiplicator=1, append_user_tag_to_data_dir=True)
def acquire(self, n_pulses, wait=False):
if getattr(self,'_sim',False):
@@ -292,19 +360,29 @@ class Jungfrau:
header_appendix['trigger_event'] = trigger_event
header_appendix['laser_pulse_energy'] = trigger_delay
header_appendix['file_prefix'] = f'run{run_number:04}-{user_tag}'
self.jfj.acquire(beam_x_pxl = loc['beam_x'], beam_y_pxl = loc['beam_y'], detector_distance_mm = detector_distance_mm, incident_energy_keV = loc['incident_energy_kev'], transmission = transmission,
sample_name = sample_name, run_number = run_number, file_prefix = jfj_file_prefix, experiment_group=pgroup, ntrigger = self.images, images_per_file = images_per_file,
unit_cell=unit_cell, space_group_number=daq_uc['space_group_number'],
header_appendix=header_appendix
)
if self.motion_mode == 6:
self.jfj.acquire(beam_x_pxl = loc['beam_x'], beam_y_pxl = loc['beam_y'], detector_distance_mm = detector_distance_mm, incident_energy_keV = loc['incident_energy_kev'], transmission = transmission,
sample_name = sample_name, run_number = run_number, file_prefix = jfj_file_prefix, experiment_group=pgroup, ntrigger = self.images, images_per_file = self.block_size_to_jungfrau,
unit_cell=unit_cell, space_group_number=daq_uc['space_group_number'],
header_appendix=header_appendix
)
else:
self.jfj.acquire(beam_x_pxl = loc['beam_x'], beam_y_pxl = loc['beam_y'], detector_distance_mm = detector_distance_mm, incident_energy_keV = loc['incident_energy_kev'], transmission = transmission,
sample_name = sample_name, run_number = run_number, file_prefix = jfj_file_prefix, experiment_group=pgroup, ntrigger = self.images, images_per_file = images_per_file,
unit_cell=unit_cell, space_group_number=daq_uc['space_group_number'],
header_appendix=header_appendix
)
_log.info('JFJ primed')
else:
is_scan_step=False
block_size = int(run['block_size']*self.bsdata_scalar) #scales block_size for bsdata acquisition only
_log.info(f'The multiplier of the block size is {self.bsdata_scalar}, new block size is {block_size}')
#_log.info(f'The multiplier of the block size is {self.bsdata_scalar}, new block size is {block_size}')
print(f'The multiplier of the block size is {self.bsdata_scalar}, new block size is {block_size}')
if type(self._daq) is CTAAcquisition:
self._daq.acquire(user_tag, n_pulses=max(n_pulses_run, block_size), n_block_size=block_size, wait=False, cell_name=run['cell_name'], is_scan_step=is_scan_step)
if self.motion_mode == 6:
self._daq.acquire(user_tag, n_pulses=max(n_pulses_run, self.block_size_to_slic), n_block_size=self.block_size_to_slic, wait=False, cell_name=run['cell_name'], is_scan_step=is_scan_step)
else:
self._daq.acquire(user_tag, n_pulses=max(n_pulses_run, block_size), n_block_size=block_size, wait=False, cell_name=run['cell_name'], is_scan_step=is_scan_step)
else:
self._daq.acquire(user_tag, n_pulses=max(n_pulses_run, block_size), n_repeat=ceil(n_pulses_run/block_size), wait=False, cell_name=run['cell_name'], is_scan_step=is_scan_step)
cfg.setValue(AppCfg.DAQ_RUN,run)