Online PyEmittance¶

The following will work either on a production system, or with a simulated EPICS server.

For local development, start a simulated EPICS server using the simulated_epics.ipynb notebook, or run in a separate process:

from pyemittance.simulation_server import start_server
start_server()

In [1]:

%load_ext autoreload
%autoreload 2

%load_ext autoreload %autoreload 2

In [2]:

from pyemittance import PyEmittance, print_logging
import numpy as np
print_logging() # Print log messages here

from pyemittance import PyEmittance, print_logging import numpy as np print_logging() # Print log messages here

In [3]:

meas = PyEmittance(config_name='LCLS2_OTR0H04')
meas.online = True

# Set some other options
meas.add_pnts = False
meas.num_points = 7   # only matters if adapt_ranges is used.
meas.adapt_ranges = True  # If helping, will ensure there are at least 7 total points
meas.check_sym = True
meas.infl_check = True

meas.show_plots = True

# Change quad bounds
meas.config_dict['meas_pv_info']['meas_device']['bounds'] = [-6, 8]

# Change settle time
meas.config_dict['meas_pv_info']['meas_device']['settle_time'] = 0.1

meas.config_dict

meas = PyEmittance(config_name='LCLS2_OTR0H04') meas.online = True # Set some other options meas.add_pnts = False meas.num_points = 7 # only matters if adapt_ranges is used. meas.adapt_ranges = True # If helping, will ensure there are at least 7 total points meas.check_sym = True meas.infl_check = True meas.show_plots = True # Change quad bounds meas.config_dict['meas_pv_info']['meas_device']['bounds'] = [-6, 8] # Change settle time meas.config_dict['meas_pv_info']['meas_device']['settle_time'] = 0.1 meas.config_dict

2023-09-02 16:00:09,852 | INFO : Initializing observer

Out[3]:

{'beamline_info': {'name': 'LCLS2',
  'species': 'electron',
  'Lquad': 0.1244,
  'energy': 80000000.0,
  'Twiss0': [1e-06, 1e-06, 5.01, 5.01, 0.049, 0.049],
  'rMatx': [1, 2.2, 0, 1],
  'rMaty': [1, 2.2, 0, 1]},
 'img_proc': {'subtract_bg': False,
  'use_roi': False,
  'avg_ims': True,
  'n_to_acquire': 1,
  'background_im': '/home/physics3/ml_tuning/20220805_LCLS2_inj/example_images/bg_8_6_22.npy',
  'amp_threshold': 150,
  'min_sigma': 3,
  'max_sigma': 700,
  'max_samples': 1,
  'roi': {'xmin': 0, 'xmax': 100, 'ymin': 0, 'ymax': 100}},
 'meas_pv_info': {'diagnostic': {'pv': {'name': 'OTRS:HTR:330',
    'image': 'OTRS:HTR:330:Image:ArrayData',
    'nrow': 'OTRS:HTR:330:Image:ArraySize1_RBV',
    'ncol': 'OTRS:HTR:330:Image:ArraySize0_RBV',
    'resolution': 'OTRS:HTR:330:RESOLUTION',
    'xsize': 'OTRS:HTR:330:XRMS',
    'ysize': 'OTRS:HTR:330:YRMS'}},
  'meas_device': {'settle_time': 0.1,
   'bounds': [-6, 8],
   'pv': {'name': 'QUAD:HTR:120',
    'cntrl': 'QUAD:HTR:120:BCTRL',
    'read': 'QUAD:HTR:120:BACT'}},
  'beam_info': {'energy': ''}},
 'savepaths': {'fits': '/home/physics3/ml_tuning/20220805_LCLS2_inj/data_saving/saved_fits/',
  'images': None,
  'monitoring': '/home/physics3/ml_tuning/20220805_LCLS2_inj/data_saving/monitoring/',
  'summaries': '/home/physics3/ml_tuning/20220805_LCLS2_inj/data_saving/summaries/',
  'raw_saves': '/home/physics3/ml_tuning/20220805_LCLS2_inj/data_saving/raw_saves/',
  'emit_saves': '/home/physics3/ml_tuning/20220805_LCLS2_inj/data_saving/emit_saves/',
  'mon_saves': '/home/physics3/ml_tuning/20220805_LCLS2_inj/data_saving/mon_saves/',
  'xopt_saves': '/home/physics3/ml_tuning/20220805_LCLS2_inj/data_saving/xopt_saves/'}}

In [4]:

meas.observer.get_beamsizes(1.2345)

meas.observer.get_beamsizes(1.2345)

Out[4]:

{'xrms': 0.0002856050839798949,
 'yrms': 0.0002720644153953202,
 'xrms_err': 0,
 'yrms_err': 0}

In [5]:

# Convenience methods.
meas.quad_init, meas.quad_bounds

# Convenience methods. meas.quad_init, meas.quad_bounds

Out[5]:

([-6, -4, -2, 0], [-6, 8])

In [6]:

meas.config_dict.keys()

meas.config_dict.keys()

Out[6]:

dict_keys(['beamline_info', 'img_proc', 'meas_pv_info', 'savepaths'])

In [7]:

meas.config_dict['meas_pv_info']['meas_device']

meas.config_dict['meas_pv_info']['meas_device']

Out[7]:

{'settle_time': 0.1,
 'bounds': [-6, 8],
 'pv': {'name': 'QUAD:HTR:120',
  'cntrl': 'QUAD:HTR:120:BCTRL',
  'read': 'QUAD:HTR:120:BACT'}}

In [8]:

meas.config_dict['img_proc']

meas.config_dict['img_proc']

Out[8]:

{'subtract_bg': False,
 'use_roi': False,
 'avg_ims': True,
 'n_to_acquire': 1,
 'background_im': '/home/physics3/ml_tuning/20220805_LCLS2_inj/example_images/bg_8_6_22.npy',
 'amp_threshold': 150,
 'min_sigma': 3,
 'max_sigma': 700,
 'max_samples': 1,
 'roi': {'xmin': 0, 'xmax': 100, 'ymin': 0, 'ymax': 100}}

In [9]:

result = meas.measure_emittance()

result = meas.measure_emittance()

2023-09-02 16:00:10,019 | INFO : Initializing observer
2023-09-02 16:00:10,021 | INFO : Running online!
2023-09-02 16:00:10,022 | INFO : EPICS put QUAD:HTR:120:BCTRL = -6
2023-09-02 16:00:10,023 | INFO : Settling for 0.1 s...
2023-09-02 16:00:11,046 | INFO : 2023-09-02_16-00-11-046232
[<pyemittance.image.Image object at 0x7f1087433790>]
2023-09-02 16:00:11,276 | INFO : EPICS put QUAD:HTR:120:BCTRL = -4
2023-09-02 16:00:11,278 | INFO : Settling for 0.1 s...
2023-09-02 16:00:11,773 | INFO : 2023-09-02_16-00-11-773604
[<pyemittance.image.Image object at 0x7f1087433790>, <pyemittance.image.Image object at 0x7f108634daf0>]
2023-09-02 16:00:11,941 | INFO : EPICS put QUAD:HTR:120:BCTRL = -2
2023-09-02 16:00:11,943 | INFO : Settling for 0.1 s...
2023-09-02 16:00:12,441 | INFO : 2023-09-02_16-00-12-441863
[<pyemittance.image.Image object at 0x7f1087433790>, <pyemittance.image.Image object at 0x7f108634daf0>, <pyemittance.image.Image object at 0x7f10bc491af0>]
2023-09-02 16:00:12,596 | INFO : EPICS put QUAD:HTR:120:BCTRL = 0
2023-09-02 16:00:12,598 | INFO : Settling for 0.1 s...
2023-09-02 16:00:13,067 | INFO : 2023-09-02_16-00-13-067086
[<pyemittance.image.Image object at 0x7f1087433790>, <pyemittance.image.Image object at 0x7f108634daf0>, <pyemittance.image.Image object at 0x7f10bc491af0>, <pyemittance.image.Image object at 0x7f1085f6d130>]
2023-09-02 16:00:13,230 | INFO : Adapting ranges
2023-09-02 16:00:13,234 | INFO : Adapting ranges for x beam size measurement: [-0.725921460376747, -0.1882678836472892, 0.3493856930821686, 0.8870392698116265, 1.4246928465410842, 1.9623464232705419, 2.5]
2023-09-02 16:00:13,235 | INFO : EPICS put QUAD:HTR:120:BCTRL = -0.725921460376747
2023-09-02 16:00:13,236 | INFO : Settling for 0.1 s...
2023-09-02 16:00:13,722 | INFO : 2023-09-02_16-00-13-722030
2023-09-02 16:00:13,890 | INFO : EPICS put QUAD:HTR:120:BCTRL = -0.1882678836472892
2023-09-02 16:00:13,892 | INFO : Settling for 0.1 s...
2023-09-02 16:00:14,416 | INFO : 2023-09-02_16-00-14-416095
2023-09-02 16:00:14,577 | INFO : EPICS put QUAD:HTR:120:BCTRL = 0.3493856930821686
2023-09-02 16:00:14,580 | INFO : Settling for 0.1 s...
2023-09-02 16:00:15,049 | INFO : 2023-09-02_16-00-15-049367
2023-09-02 16:00:15,212 | INFO : EPICS put QUAD:HTR:120:BCTRL = 0.8870392698116265
2023-09-02 16:00:15,215 | INFO : Settling for 0.1 s...
2023-09-02 16:00:15,748 | INFO : 2023-09-02_16-00-15-748219
2023-09-02 16:00:15,903 | INFO : EPICS put QUAD:HTR:120:BCTRL = 1.4246928465410842
2023-09-02 16:00:15,905 | INFO : Settling for 0.1 s...
2023-09-02 16:00:16,369 | INFO : 2023-09-02_16-00-16-369151
2023-09-02 16:00:16,525 | INFO : EPICS put QUAD:HTR:120:BCTRL = 1.9623464232705419
2023-09-02 16:00:16,527 | INFO : Settling for 0.1 s...
2023-09-02 16:00:16,990 | INFO : 2023-09-02_16-00-16-990638
2023-09-02 16:00:17,151 | INFO : EPICS put QUAD:HTR:120:BCTRL = 2.5
2023-09-02 16:00:17,154 | INFO : Settling for 0.1 s...
2023-09-02 16:00:17,731 | INFO : 2023-09-02_16-00-17-731145
2023-09-02 16:00:17,898 | INFO : Adapting ranges for y beam size measurement: [-1.811576315025631, -1.0929802625213592, -0.3743842100170873, 0.3442118424871845, 1.0628078949914563, 1.7814039474957282, 2.5]
2023-09-02 16:00:17,900 | INFO : EPICS put QUAD:HTR:120:BCTRL = -1.811576315025631
2023-09-02 16:00:17,901 | INFO : Settling for 0.1 s...
2023-09-02 16:00:18,383 | INFO : 2023-09-02_16-00-18-383328
2023-09-02 16:00:18,537 | INFO : EPICS put QUAD:HTR:120:BCTRL = -1.0929802625213592
2023-09-02 16:00:18,540 | INFO : Settling for 0.1 s...
2023-09-02 16:00:19,021 | INFO : 2023-09-02_16-00-19-021105
2023-09-02 16:00:19,182 | INFO : EPICS put QUAD:HTR:120:BCTRL = -0.3743842100170873
2023-09-02 16:00:19,183 | INFO : Settling for 0.1 s...
2023-09-02 16:00:19,666 | INFO : 2023-09-02_16-00-19-666574
2023-09-02 16:00:19,835 | INFO : EPICS put QUAD:HTR:120:BCTRL = 1.0628078949914563
2023-09-02 16:00:19,837 | INFO : Settling for 0.1 s...
2023-09-02 16:00:20,302 | INFO : 2023-09-02_16-00-20-302784
2023-09-02 16:00:20,588 | INFO : EPICS put QUAD:HTR:120:BCTRL = 1.7814039474957282
2023-09-02 16:00:20,591 | INFO : Settling for 0.1 s...
2023-09-02 16:00:21,069 | INFO : 2023-09-02_16-00-21-069003
2023-09-02 16:00:21,071 | INFO : Beam params out of bounds in image 0 out of 1 samples
2023-09-02 16:00:21,234 | INFO : Resampled 0 times (max_samples = 1, beam still out of bounds 

2023-09-02 16:00:21,238 | INFO : xrms 57.62 um, yrms 708.39 um (threshold: min_rms 60.60 um, max_rms 14140.00 um)
2023-09-02 16:00:21,240 | INFO : xamp 699418.11, yamp 56932.53 (amp_thresh: 150, in json)
2023-09-02 16:00:21,241 | INFO : area_x 104912717.2, area_y 8539879.0 (threshold: 1500, hardcoded)

2023-09-02 16:00:21,243 | INFO : Returning NaNs
2023-09-02 16:00:21,245 | INFO : Checking symmetry
2023-09-02 16:00:21,247 | INFO : EPICS put QUAD:HTR:120:BCTRL = 2.960845922910964
2023-09-02 16:00:21,254 | INFO : Settling for 0.1 s...
2023-09-02 16:00:21,739 | INFO : 2023-09-02_16-00-21-738973
2023-09-02 16:00:21,918 | INFO : EPICS put QUAD:HTR:120:BCTRL = 3.575307153458916
2023-09-02 16:00:21,920 | INFO : Settling for 0.1 s...
2023-09-02 16:00:22,377 | INFO : 2023-09-02_16-00-22-377582
2023-09-02 16:00:22,535 | INFO : EPICS put QUAD:HTR:120:BCTRL = 4.189768384006868
2023-09-02 16:00:22,539 | INFO : Settling for 0.1 s...
2023-09-02 16:00:23,001 | INFO : 2023-09-02_16-00-23-001832
2023-09-02 16:00:23,170 | INFO : EPICS put QUAD:HTR:120:BCTRL = 4.80422961455482
2023-09-02 16:00:23,174 | INFO : Settling for 0.1 s...
2023-09-02 16:00:23,642 | INFO : 2023-09-02_16-00-23-642348
2023-09-02 16:00:23,804 | INFO : EPICS put QUAD:HTR:120:BCTRL = 3.1159394735750903
2023-09-02 16:00:23,806 | INFO : Settling for 0.1 s...
2023-09-02 16:00:24,280 | INFO : 2023-09-02_16-00-24-280537
2023-09-02 16:00:24,600 | INFO : EPICS put QUAD:HTR:120:BCTRL = 3.9371921050085437
2023-09-02 16:00:24,603 | INFO : Settling for 0.1 s...
2023-09-02 16:00:25,075 | INFO : 2023-09-02_16-00-25-075346
2023-09-02 16:00:25,231 | INFO : EPICS put QUAD:HTR:120:BCTRL = 5.5796973678754505
2023-09-02 16:00:25,233 | INFO : Settling for 0.1 s...
2023-09-02 16:00:25,734 | INFO : 2023-09-02_16-00-25-734743
2023-09-02 16:00:25,893 | INFO : Checking inflection
2023-09-02 16:00:25,895 | INFO : Emmitance calc for 11 x points, 11 y points

Examine results¶

In [10]:

import matplotlib.pyplot as plt

import matplotlib.pyplot as plt

In [11]:

result

result

Out[11]:

{'quadvalsx': array([-0.72592146, -0.18826788,  0.34938569,  0.88703927,  1.42469285,
         1.96234642,  2.5       ,  2.96084592,  3.57530715,  4.18976838,
         4.80422961]),
 'beamsizesx': array([5.31078936e-04, 4.16967250e-04, 3.00199679e-04, 1.87642596e-04,
        8.65015138e-05, 7.40842698e-05, 1.71003369e-04, 2.62990146e-04,
        3.89370174e-04, 5.15351284e-04, 6.37011245e-04]),
 'beamsizeserrx': array([6.23146215e-07, 3.90894651e-07, 2.63595986e-07, 1.18694232e-07,
        2.89670715e-08, 3.39773933e-08, 9.45749799e-08, 1.97634824e-07,
        3.77245628e-07, 5.77603650e-07, 8.91494299e-07]),
 'error_x': False,
 'emit_x': 6.380225302143409e-09,
 'norm_emit_x': 9.988427795017674e-07,
 'beta_x': 10.028119862136135,
 'alpha_x': -2.0149667431522307,
 'emit_x_err': 3.584955433519756e-12,
 'norm_emit_x_err': 5.612351727459969e-10,
 'beta_x_rel_err': 0.000561885398046273,
 'alpha_x_rel_err': -3.2106833809592616e-20,
 'sigma_11': 6.398166407732784e-08,
 'sigma_12': 1.2855941797637363e-08,
 'sigma_22': 3.219399141625969e-09,
 'screen_sigma_11': array([2.83971546e-07, 1.73221599e-07, 9.06662915e-08, 3.56348101e-08,
        7.46511500e-09, 5.50386039e-09, 2.91063180e-08, 6.92011534e-08,
        1.50466086e-07, 2.62660888e-07, 4.04874363e-07]),
 'screen_sigma_12': array([ 6.55439337e-08,  2.98877193e-08,  6.59080634e-09, -4.64501801e-09,
        -4.11404248e-09,  7.89333347e-09,  3.10905651e-08,  5.96657053e-08,
         1.09927484e-07,  1.73711680e-07,  2.50613466e-07]),
 'screen_sigma_22': array([1.52716516e-08, 5.39183937e-09, 9.28084757e-10, 1.74782655e-09,
        7.72025889e-09, 1.87163156e-08, 3.46086547e-08, 5.20324227e-08,
        8.05813407e-08, 1.15039797e-07, 1.55227948e-07]),
 'quadvalsy': array([-1.81157632, -1.09298026, -0.37438421,  0.34421184,  1.06280789,
         2.5       ,  3.11593947,  3.93719211,  4.75844474,  5.57969737]),
 'beamsizesy': array([0.00171271, 0.00151594, 0.0013238 , 0.00110886, 0.00091245,
        0.0004951 , 0.00031929, 0.00010643, 0.00022087, 0.00044845]),
 'beamsizeserry': array([4.42851438e-06, 3.80479429e-06, 3.08277465e-06, 2.46012153e-06,
        1.61680594e-06, 7.53839455e-07, 3.65935103e-07, 4.77619333e-08,
        1.74149531e-07, 4.92537533e-07]),
 'error_y': False,
 'emit_y': 1.3751948236228059e-08,
 'norm_emit_y': 2.152907389528063e-06,
 'beta_y': 10.397064147488576,
 'alpha_y': 18.80069944220473,
 'emit_y_err': 1.344717956408853e-11,
 'norm_emit_y_err': 2.105194969798521e-09,
 'beta_y_rel_err': 0.000977838145772363,
 'alpha_y_rel_err': 2.804075932518792e-19,
 'sigma_33': 1.4297988796500551e-07,
 'sigma_34': -2.585462455340812e-07,
 'sigma_44': 4.688441018814357e-07,
 'screen_sigma_33': array([2.96366364e-06, 2.31644175e-06, 1.74285170e-06, 1.24574977e-06,
        8.28046203e-07, 2.42748957e-07, 9.87886497e-08, 1.13466513e-08,
        4.77042107e-08, 2.12716246e-07]),
 'screen_sigma_34': array([ 1.56456893e-06,  1.24908096e-06,  9.65716734e-07,  7.15744832e-07,
         5.00457982e-07,  1.79232797e-07,  8.83277978e-08,  1.28770548e-08,
        -8.34102735e-09,  2.68316655e-08]),
 'screen_sigma_44': array([8.26026617e-07, 6.73616062e-07, 5.35213596e-07, 4.11382601e-07,
        3.02697249e-07, 1.33114935e-07, 8.08890087e-08, 3.12810019e-08,
        5.42276696e-09, 4.27355394e-09]),
 'sqrt_norm_emit_4d': 1.4664296781523841e-06,
 'sqrt_norm_emit_4d_err': 1.6538067541652102e-09}

In [12]:

plt.plot(result['quadvalsx'], np.sqrt(result['screen_sigma_11']))
plt.plot(result['quadvalsx'], result['beamsizesx'], marker='x')

plt.plot(result['quadvalsx'], np.sqrt(result['screen_sigma_11'])) plt.plot(result['quadvalsx'], result['beamsizesx'], marker='x')

Out[12]:

[<matplotlib.lines.Line2D at 0x7f105b7ef1c0>]

In [13]:

plt.plot(result['quadvalsy'], np.sqrt(result['screen_sigma_33']))
plt.plot(result['quadvalsy'], result['beamsizesy'], marker='x')

plt.plot(result['quadvalsy'], np.sqrt(result['screen_sigma_33'])) plt.plot(result['quadvalsy'], result['beamsizesy'], marker='x')

Out[13]:

[<matplotlib.lines.Line2D at 0x7f105b8b12b0>]

Observer¶

The observer keeps all measurements made, as well as extra information such as images.

In [14]:

o = meas.observer
o.beam_meas['x']

o = meas.observer o.beam_meas['x']

Out[14]:

[0.0017319965094041647,
 0.0012677116067485394,
 0.0008156152128438839,
 0.0007717229143932074,
 0.0006109280395657084,
 0.0005310789363652958,
 0.0004565024520392191,
 0.00041696725034169694,
 0.00037389685405919346,
 0.0003001996785587896,
 0.00018764259633947025,
 0.0001527761765133468,
 8.650151376800355e-05,
 nan,
 7.408426981944035e-05,
 0.0001710033694494241,
 0.0002629901458582531,
 0.00029583871423323097,
 0.0003893701741397189,
 0.0004609075071683442,
 0.0005153512835542348,
 0.0006370112451163578,
 0.0007952563299734706]

In [15]:

# Note that this was a problematic image
ix_nan = np.where(np.isnan(o.beam_meas['x']))[0][0]
ix_nan

# Note that this was a problematic image ix_nan = np.where(np.isnan(o.beam_meas['x']))[0][0] ix_nan

Out[15]:

13

In [16]:

# This is the image
o.extra[ix_nan].get_sizes()

# This is the image o.extra[ix_nan].get_sizes()

Out[16]:

{'xrms': 2.8522865575268885,
 'yrms': 35.06890802299145,
 'xrms_err': 0.0010253071845839176,
 'yrms_err': 0.05845542290783643,
 'xamp': 699418.1145178082,
 'yamp': 56932.52655505132}

In [17]:

# The observer can also set the quad and return sizes (and extra image).
dat = o.get_beamsizes(1.2345)
dat

# The observer can also set the quad and return sizes (and extra image). dat = o.get_beamsizes(1.2345) dat

2023-09-02 16:00:27,428 | INFO : EPICS put QUAD:HTR:120:BCTRL = 1.2345
2023-09-02 16:00:27,430 | INFO : Settling for 0.1 s...
2023-09-02 16:00:27,895 | INFO : 2023-09-02_16-00-27-895549

Out[17]:

{'xrms': 0.00012047477546215778,
 'yrms': 0.0008570228573263447,
 'xrms_err': 5.86217973346717e-08,
 'yrms_err': 1.528657218869215e-06,
 'extra': <pyemittance.image.Image at 0x7f105b696400>}

In [18]:

# This is the image
im = dat['extra']
im

# This is the image im = dat['extra'] im

Out[18]:

<pyemittance.image.Image at 0x7f105b696400>

In [19]:

# This plots. TODO: make a .plot() instead
im.get_sizes()

# This plots. TODO: make a .plot() instead im.get_sizes()

Out[19]:

{'xrms': 5.964097795156326,
 'yrms': 42.42687412506657,
 'xrms_err': 0.0029020691749837477,
 'yrms_err': 0.07567609994402054,
 'xamp': 334856.0390775527,
 'yamp': 46946.04587345442}

Interactively change the quad and acquire the screen image¶

In [20]:

import epics
import matplotlib.pyplot as plt

from ipywidgets import interact

def f(quad_value):
    epics.caput('QUAD:HTR:120:BCTRL', quad_value)
    a = epics.caget('OTRS:HTR:330:Image:ArrayData').reshape(1040, 1392)
    sigma_x = epics.caget('sim_screen_sigma_x')
    sigma_y = epics.caget('sim_screen_sigma_y')  
    print(sigma_x)
    plt.imshow(a, vmax=128)
    plt.title(f'sim sigma_x, y = {sigma_x*1e3:0.3f}    {sigma_y*1e3:0.3f} mm')
    
# interact(f, quad_value=(-4, 4, .1))    
f(0)

import epics import matplotlib.pyplot as plt from ipywidgets import interact def f(quad_value): epics.caput('QUAD:HTR:120:BCTRL', quad_value) a = epics.caget('OTRS:HTR:330:Image:ArrayData').reshape(1040, 1392) sigma_x = epics.caget('sim_screen_sigma_x') sigma_y = epics.caget('sim_screen_sigma_y') print(sigma_x) plt.imshow(a, vmax=128) plt.title(f'sim sigma_x, y = {sigma_x*1e3:0.3f} {sigma_y*1e3:0.3f} mm') # interact(f, quad_value=(-4, 4, .1)) f(0)

0.00037486171231124573