Plasma column position¶

Adapted version of InnerStabilisation.ipynb by Daniela Kropáčková, Honza Stöckel and Vojtěch Svoboda.

This notebook loads Mirnov coil data and calculates the plasma column position from them. It also calculates the plasma column position from the fast camera data and compares the two diagnostics.

Import libraries¶

import os

#delete files from the previous discharge
if os.path.exists('InnerStabilization.html'):
    os.remove('InnerStabilization.html')
    
if os.path.exists('video.mp4'):
    os.remove('video.mp4')
if os.path.exists('icon-fig.png'):
    os.remove('icon-fig.png')

import numpy as np
import matplotlib.pyplot as plt

from scipy import integrate, signal, interpolate
import pandas as pd


import holoviews as hv
hv.extension('bokeh')
import hvplot.pandas
import requests

from IPython.display import Markdown

#execute time
from timeit import default_timer as timer
start_execute = timer()

Set discharge number¶

To calculate the plasma position, $B_t$ contribution must be subtracted from the Mirnov coil signal. This contribution can be acquired by two ways: from a dedicated vacuum shot with the same toroidal magnetic field, or it can be estimated from the standard diagnostics. If a suitable vacuum shot is available, its number is stored in the variable vacuum_shot. If it isn't available, the vacuum_shot variable shall be set to False and the $B_t$ contribution shall be estimated.

# data_URL = "http://golem.fjfi.cvut.cz/shots/{shot_no}/DASs/LimiterMirnovCoils/{identifier}.csv"  #Mirnov coils and quadrupole
BDdata_URL = "http://golem.fjfi.cvut.cz/shots/{shot_no}/Diagnostics/BasicDiagnostics/{identifier}.csv" #BD = basic diagnostic
# data_URL = "http://golem.fjfi.cvut.cz/shots/{shot_no}/DASs/022Daniela0InnerStabilization/{identifier}.csv"  
data_URL = "http://golem.fjfi.cvut.cz/shots/{shot_no}/Diagnostics/LimiterMirnovCoils/DAS_raw_data_dir/Nidatap_6133.lvm" #NI Standart (DAS)

shot_no = 35362 # to be replaced by the actual discharge number
#shot_no = 35021
vacuum_shot = 35353 # to be replaced by the discharge command line paramater "vacuum_shot"
#vacuum_shot = 35022 #number of the vacuum shot or 'False'

ds = np.DataSource(destpath='')

Data access¶

def open_remote(shot_no, identifier, url_template=data_URL):
    return ds.open(url_template.format(shot_no=shot_no, identifier=identifier))

def read_signal(shot_no, identifier, url = data_URL, data_type='csv'): 
    file = open_remote(shot_no, identifier, url)
    if data_type == 'lvm':
        channels = ['Time', 'mc1', 'mc5', 'mc9', 'mc13', '5', 'RogQuadr', '7', '8', '9', '10', '11', '12']
        return pd.read_table(file, sep = '\t', names=channels)
    else:
        return pd.read_csv(file, names=['Time', identifier],
                     index_col = 'Time', squeeze=True)

def get_basic_diag_data(shot):
    url = ( 'http://golem.fjfi.cvut.cz/shots/{}/Diagnostics/BasicDiagnostics/'
            'basig_diagnostics_processed.csv'.format(shot) )
    print(url)
    return pd.read_csv(url, header=0, index_col='Time')

Mirnov coil signal processing: integration and $B_t$ elimination¶

Load the data of a given Mirnov coil, integrate it and subtract the $B_t$ contribution from them.

def elimination (shot_no, identifier, vacuum_shot = False):
    #load data 
    mc = (read_signal(shot_no, identifier, data_URL, 'lvm'))
    mc = mc.set_index('Time')
    mc = mc.replace([np.inf, -np.inf, np.nan], value = 0)
    mc = mc[identifier]
    
    konst = 1/(3.8e-03)

    if vacuum_shot == False: 
        signal_start = mc.index[0]
        length = len(mc)
        basic_diag = get_basic_diag_data(shot_no)
        Bt = basic_diag['Bt']
        if len(Bt)>len(mc):
            Bt = Bt.iloc[:length]            
        if len(Bt)<len(mc):
            mc = mc.iloc[:len(Bt)]
        
        if identifier == 'mc1':
            k=300
        elif identifier == 'mc5':
            k= 14
        elif identifier == 'mc9':
            k = 31
        elif identifier == 'mc13':
            k = -100 
        
        mc_vacuum = Bt/k
    else:
        mc_vacuum = (read_signal(vacuum_shot, identifier, data_URL, 'lvm'))
        mc_vacuum = mc_vacuum.set_index('Time')
        mc_vacuum = mc_vacuum[identifier]
        mc_vacuum -= mc_vacuum.loc[:0.9e-3].mean()    #remove offset
        mc_vacuum = mc_vacuum.replace([np.inf, -np.inf], value = 0)
        
        mc_vacuum = pd.Series(integrate.cumtrapz(mc_vacuum, x=mc_vacuum.index, initial=0) * konst,
                    index=mc_vacuum.index*1000, name= identifier)    #integration

    mc -= mc.loc[:0.9e-3].mean()  #remove offset
       
    mc = pd.Series(integrate.cumtrapz(mc, x=mc.index, initial=0) * konst,
                    index=mc.index*1000, name= identifier)    #integration
    
    #Bt elimination
    mc_vacuum = np.array(mc_vacuum) 
    mc_elim = mc - mc_vacuum
    
    return mc_elim

Find plasma start and end¶

Find plasma start and end from the basic diagnostics.

loop_voltage = read_signal(shot_no, 'U_Loop', BDdata_URL)

dIpch = read_signal(shot_no, 'U_RogCoil', BDdata_URL)

dIpch -= dIpch.loc[:0.9e-3].mean()

Ipch = pd.Series(integrate.cumtrapz(dIpch, x=dIpch.index, initial=0) * (-5.3*1e06),
                index=dIpch.index, name='Ipch')

U_l_func = interpolate.interp1d(loop_voltage.index, loop_voltage)  
def dIch_dt(t, Ich):
    return (U_l_func(t) - 0.0097 * Ich) / (1.2e-6/2)
t_span = loop_voltage.index[[0, -1]]
solution = integrate.solve_ivp(dIch_dt, t_span, [0], t_eval=loop_voltage.index, )
Ich = pd.Series(solution.y[0], index=loop_voltage.index, name='Ich')
Ip = Ipch - Ich
Ip.name = 'Ip'

Ip_detect = Ip.loc[0.0025:]

dt = (Ip_detect.index[-1] - Ip_detect.index[0]) / (Ip_detect.index.size) 

window_length = int(0.5e-3/dt)  
if window_length % 2 == 0:  
    window_length += 1
dIp = pd.Series(signal.savgol_filter(Ip_detect, window_length, polyorder=3, deriv=1, delta=dt),
                name='dIp', index=Ip_detect.index) / 1e6 

threshold = 0.05

CD = requests.get("http://golem.fjfi.cvut.cz/shots/%i/Production/Parameters/CD_orientation" % shot_no)
CD_orientation = CD.text

if "ACW" in CD_orientation:
    plasma_start = dIp[dIp < dIp.min()*threshold].index[0]*1e3 
    plasma_end = dIp.idxmax()*1e3 
else: 
    plasma_start = dIp[dIp > dIp.max()*threshold].index[0]*1e3 
    plasma_end = dIp.idxmin()*1e3 + 0.5    


print ('Plasma start =', round(plasma_start, 3), 'ms')
print ('Plasma end =', round(plasma_end, 3), 'ms')
# print (CD_orientation)

Plasma start = 2.501 ms
Plasma end = 18.236 ms

mc1 = elimination(shot_no, 'mc1', vacuum_shot)

Horizontal plasma position $\Delta r$ calculation¶

def horpol(shot_no, vacuum_shot=False):
    mc1 = elimination(shot_no, 'mc1', vacuum_shot)
    mc9 = elimination (shot_no, 'mc9', vacuum_shot)
    
    b = 93
    
    r = ((mc1-mc9)/(mc1+mc9))*b
    r = r.replace([np.nan], value = 0)
    
#     return r.loc[plasma_start:]
    return r.loc[plasma_start:plasma_end]
#     return r

r = horpol(shot_no, vacuum_shot)
ax = r.plot()
ax.set(ylim=(-85,85), xlim=(plasma_start,plasma_end), xlabel= 'Time [ms]', ylabel = '$\Delta$r [mm]',
       title = 'Horizontal plasma position #{}'.format(shot_no))
ax.axhline(y=0, color='k', ls='--', lw=1, alpha=0.4)

<matplotlib.lines.Line2D at 0x7fd4c406d4d0>

Vertical plasma position $\Delta z$ calculation¶

def vertpol(shot_no, vacuum_shot = False):
    mc5 = elimination(shot_no, 'mc5', vacuum_shot)
    mc13 = elimination (shot_no, 'mc13', vacuum_shot)
    
    b = 93
    
    z = ((mc5-mc13)/(mc5+mc13))*b
    z = z.replace([np.nan], value = 0)
#     return z.loc[plasma_start:]
    return z.loc[plasma_start:plasma_end]
#     return z

z = vertpol (shot_no, vacuum_shot)
ax = z.plot()
ax.set(ylim=(-85, 85), xlim=(plasma_start,plasma_end), xlabel= 'Time [ms]', ylabel = '$\Delta$z [mm]', title = 'Vertical plasma position #{}'.format(shot_no))
ax.axhline(y=0, color='k', ls='--', lw=1, alpha=0.4)

<matplotlib.lines.Line2D at 0x7fd4b85e4410>

Plasma column radius $a$ calculation¶

def plasma_radius(shot_no, vacuum_shot=False):
    r = horpol(shot_no, vacuum_shot) 
    z = vertpol(shot_no, vacuum_shot) 
    
    a0 = 85
    a = a0 - np.sqrt((r**2)+(z**2)) 
    a = a.replace([np.nan], value = 0)
#     return a.loc[plasma_start:]
    return a.loc[plasma_start:plasma_end]
#     return a

a = plasma_radius(shot_no,vacuum_shot)
ax = a.plot()
ax.set(ylim=(0,85), xlim=(plasma_start,plasma_end), xlabel= 'Time [ms]', ylabel = '$a$ [mm]', title = 'Plasma column radius #{}'.format(shot_no))

[(0, 85),
 Text(0, 0.5, '$a$ [mm]'),
 (2.50064728, 18.2356473),
 Text(0.5, 0, 'Time [ms]'),
 Text(0.5, 1.0, 'Plasma column radius #35362')]

Save the results¶

plasma_time = []
t = 0
for i in a:
    if i>85 or i <0:
        a = a.replace(i, value = 0)
    else:

        plasma_time.append(a.index[t])

    t+=1
start = plasma_time[0]-1e-03 
end = plasma_time[-1]-1e-03 
print('start =', round(start, 3), 'ms')
print('end =', round(end, 3), 'ms')

start = 5.92 ms
end = 17.662 ms

r_cut = r.loc[start:end]
a_cut = a.loc[start:end]
z_cut = z.loc[start:end]
df_processed = pd.concat(
    [r_cut.rename('r'), z_cut.rename('z'), a_cut.rename('a')], axis= 'columns')
df_processed

savedata = 'plasma_position.csv'
df_processed.to_csv(savedata)

Markdown("[Plasma position data - $r, z, a$ ](./{})".format(savedata))

Plot the results¶

hline = hv.HLine(0)
hline.opts(
    color='k', 
    line_dash='dashed',
    alpha = 0.4,
    line_width=1.0)

layout = hv.Layout([df_processed[v].hvplot.line(
    xlabel='', ylabel=l,ylim=(-85,85), xlim=(start,end),legend=False, title='', grid=True, group_label=v)
                    for (v, l) in [('r', ' r [mm]'), ('z', 'z [mm]'), ('a', 'a [mm]')] ])*hline

plot=layout.cols(1).opts(hv.opts.Curve(width=600, height=200),  
                    hv.opts.Curve('a', xlabel='time [ms]'))
plot

fig, axs = plt.subplots(3, 1, sharex=True, dpi=200)
r.plot(grid=True, ax=axs[0])
z.plot(grid=True, ax=axs[1])
a.plot(grid=True, ax=axs[2])
axs[2].set(ylim=(0,85), xlim=(start,end), xlabel= 'Time [ms]', ylabel = '$a$ [mm]')
axs[1].set(ylim=(-85,85), xlim=(start,end), xlabel= 'Time [ms]', ylabel = '$\Delta$z [mm]')
axs[0].set(ylim=(-85,85), xlim=(start,end), xlabel= 'Time [ms]', ylabel = '$\Delta$r [mm]', title = 'Horizontal, vertical plasma position and radius #{}'.format(shot_no))


plt.savefig('icon-fig')

Fast cameras¶

The plasma vertical position can also be calculated from the fast camera signal as the centre of the radiating zone.

from PIL import Image
from io import BytesIO
from IPython.display import Image as DispImage

FastCamera = True


try:
    url = "http://golem.fjfi.cvut.cz/shots/%i/Diagnostics/FastExCameras/plasma_film.png"%(shot_no)
    image = requests.get(url)
    img = Image.open(BytesIO(image.content)).convert('P') #'L','1'

    data = np.asanyarray(img)

    r = []
    for i in range(data.shape[1]):
        a=0
        b=0
        for j in range(336):
            a += data[j,i]*j
            b += data[j,i]
        r.append((a/b)*(170/336))
    Tcd = 3 #delay
    camera_time = np.linspace(start+abs(start-Tcd), end, len(r))
    r_camera = pd.Series(r, index = camera_time)-85
    r_mirnov = horpol(shot_no, vacuum_shot).loc[start:end]
#     print(start, end, len(r))
        
    fig = plt.figure()
    ax = r_camera.plot(label = 'Fast Camera')
    ax = r_mirnov.plot(label = 'Mirnov coils')
    plt.legend()
    ax.set(ylim=(-85, 85), title='#%i'%shot_no,ylabel='$\Delta$r visible radiation')
    ax.axhline(y=0, color='k', ls='--', lw=1, alpha=0.4)
    fig.savefig('FastCameras_deltaR')
except OSError:
    FastCamera = False

if FastCamera == True:
    plt.imshow(img)

	r	z	a
Time
5.920	55.091067	-64.758770	0.000000
5.921	54.966092	-64.373656	0.352266
5.922	54.810273	-64.016853	0.724716
5.923	54.614996	-63.725820	1.072782
5.924	54.410052	-63.558750	1.332991
...	...	...	...
17.657	2.336332	-36.413212	48.511913
17.658	2.259115	-47.333866	37.612254
17.659	-0.218440	-51.479860	33.519676
17.660	2.285844	-53.456803	31.494347
17.661	9.125382	-58.193700	26.095167