if os.path.exists('orb') == True:
os.remove('orb')
print("./orb directory has been removed.")
parser = AG.ArgumentParser()
parser.add_argument("control_file",
nargs='?',
help="Control file ",
default='control.data')
args = parser.parse_args()
# open control file
p_file = args.control_file
pf = PF.pfile(p_file)
machine = pf.get_value('machine')
input_root = pf.get_value('input_root')
input_dir_ext = pf.get_value('input_dir_ext')
input_dir = input_root + machine + input_dir_ext + '/'
input_file = pf.get_value('input_file')
input_name = input_dir + input_file
input_ext = pf.get_value('nml_ext')
A = z_prime/(np.sqrt(x_prime**2 + z_prime**2))
return np.arccos(A)/dtr
#########################Proper Files###############
# reverse direction
reverse = False
parser = AG.ArgumentParser()
parser.add_argument("control_file", nargs = '?', help="Control file ", default = 'control.data')
args = parser.parse_args()
# open control file
c_file = args.control_file
cd = PF.pfile(c_file)
machine = cd.get_value('machine')
input_root = cd.get_value('input_root')
input_dir_ext = cd.get_value('input_dir_ext')
nml_dir = input_root + machine + input_dir_ext + '//'
#nml_filename = 'MAST_p6'
nml_filename = cd.get_value('input_file')
make_new_nml = cd.get_value('make_new_nml', var_type = cd.Bool)
#static_dir = 'MAST_input'
h_file = data_dir + 'header_comments.data'
s_file = data_dir + 'small_R.data'
files = [\
'large_R_0.data',\
'large_R_01.data',\
'large_R_11.data',\
'large_R_02.data',\
'large_R_2.data',\
'large_R_3.data',\
'large_R_4.data',\
'large_R_5.data',\
'large_R_6.data']
cd = pfile(h_file)
rl = []
zl = []
phil = []
comments = []
# large R data
for fn in files:
f = data_dir + fn
d = B.get_file(f)
rl.append(B.get_data(d, 'r'))
zl.append(B.get_data(d, 'z'))
phil.append(d.par.get_value('phi'))
comments.append(d.par.get_value('comment'))
rl = np.array(rl)
def main(control_file, output_folder, vlen):
global plot_command
# open control file and read parameters
c_file = control_file
cd = PF.pfile(c_file)
dynamic_dir = cd.get_value('dynamic_dir')
dyn_file = cd.get_value('dynamic_file')
plot_command = cd.get_value('plot_command') + ' ' + c_file
##########################Obtaining Parameters and Data########################
# Grabbing dynamic data file
dd = B.get_file(dynamic_dir + dyn_file)
dpar = dd.par
# get the assigned detectors ids
detector_id = B.get_data(dd, 'detector_id')
# total number of detectors in dynamic file
N_det = len(detector_id)
# Port angle of each detector when the Reciprocating probe arm is at a rotation angle of 0, convert to rads
ppb = B.get_data(dd, 'phi_port_base')*dtr
# Theta angle of each detector when the Reciprocating
# probe arm is at a rotation angle of 0
# Port angle was input in degrees
tpb = B.get_data(dd, 'theta_port_base')*dtr
# Horizontal offset, from the center of the diagnostic, of each detector
# Horizontal offset was input in mm
dyo = B.get_data(dd, 'detector_horizontal_offset')*mm2m
# Radial offset of each detector (measured from the base)
# Radial offset was input in mm
dro = B.get_data(dd, 'detector_radial_axis_offset')*mm2m
# Height offset of each detector (measured from the center)
# Height offset was input in mm
dzo = B.get_data(dd, 'detector_height_offest')*mm2m
# detector type (Probe or Fixed)
det_type = B.get_data(dd, 'det_type')
# Alpha is the rotational angle of the RP arm
# converted to radians
alpha = dpar.get_value('RP_rotation')*dtr
##############################Making Calculations##########################
# indexes of fixed detectors
fixed_dets = np.where(det_type == 'Fixed')
# calculation of positions change for each Probe detector due to rotation
dyor = np.sqrt(dyo**2 + dzo**2)*np.cos(alpha + pol_angle(dyo, dzo))
dzor = np.sqrt(dyo**2 + dzo**2)*np.sin(alpha + pol_angle(dyo, dzo))
# RDist is the distance from the center of the tokamak to each detector (m)
RDist = np.sqrt((dpar.get_value('RDist') + dro + dpar.get_value('RDist_offset'))**2 + dyor**2)
RDist[fixed_dets] = dro[fixed_dets]
# ZDist here is the height of each detector relative to the centr of the
# tokamak, in dynamic file ZDist is RP position hight
ZDist = dpar.get_value('ZDist') + dzor
ZDist[fixed_dets] = dzor[fixed_dets]
#RP phd angle
RP_phd = dpar.get_value('PHDangle')
# PHD angle shift for each detector relative to RP_phd
dphd= np.arcsin(dyor/RDist)/dtr
# phdangle is the toroidal angle of each detector in radians
phdangle = RP_phd + dphd
phdangle[fixed_dets] = dyo[fixed_dets]
# The following are the calculations for the change in phi and theta angles
phi_port, theta_port = rotate_det(ppb, tpb, alpha, dphd*dtr)
phi_port /= dtr
theta_port /= dtr
phi_port[fixed_dets] = ppb[fixed_dets]/dtr
theta_port[fixed_dets] = tpb[fixed_dets]/dtr
for k in range(N_det):
geom = open(output_folder + 'track' + str(k)+ '.dat', 'w')
xx=RDist[k]*np.cos(phdangle[k])
yy=RDist[k]*np.sin(phdangle[k])
zz=ZDist[k]
geom.write('{} {} {}\n'.format(xx,yy,zz))
print(xx, yy, zz)
vx = -vlen*np.cos(phi_port[k]*dtr)*np.sin(theta_port[k]*dtr)
vy = -vlen*np.sin(phi_port[k]*dtr)
vz = vlen*np.cos(phi_port[k]*dtr)*np.cos(theta_port[k]*dtr)
print("V", vx, vy, vz)
v1 = vx*np.cos(phdangle[k]*dtr) - vy*np.sin(phdangle[k]*dtr)
v2 = vx*np.sin(phdangle[k]*dtr) + vy*np.cos(phdangle[k]*dtr)
v3 = vz
print("Vr", v1,v2,v3)
xx = xx + v1
yy = yy + v2
zz = zz + v3
print(xx, yy, zz)
geom.write('{} {} {}\n'.format(xx,yy,zz))
geom.close()
def main(c_file):
control_file = c_file
# contpour plotting controle
cont_scale = 1.0
ncont = 25
#colormap = pl.get_cmap('CMRmap')
#colormap = pl.get_cmap('gnuplot')
#colormap = pl.get_cmap('gnuplot2')
colormap = pl.get_cmap('gist_heat')
#colormap = pl.get_cmap('jet')
#colormap = pl.get_cmap('hot')
# open control file
p_file = control_file
pf = PF.pfile(p_file)
output_dir = pf.get_value('output_dir')
# ???
plot_em = pf.get_value('plot_em', var_type=pf.Bool)
# ??
em_filled = pf.get_value('em_filled', var_type=pf.Bool)
# ??
plot_psirel = pf.get_value('plot_psirel', var_type=pf.Bool)
# ??
psirel_filled = pf.get_value('psirel_filled', var_type=pf.Bool)
##
all_yellow = pf.get_value('all_yellow', var_type=pf.Bool)
# color array
if all_yellow:
colors = ['y', 'y', 'y', 'y', 'y', 'y', 'y', 'y', 'y',
'y'] # make everything yellow
else:
colors = [
'red', 'green', 'blue', 'yellow', 'magenta', 'cyan', 'orange',
'lavenderblush', 'maroon', 'plum'
]
# dynamic input file for detector/channels assignment
di_dir = pf.get_value('dynamic_dir')
di_file = pf.get_value('dynamic_file')
dynamic_file = di_dir + di_file
df = B.get_file(dynamic_file)
dfd = df.par
# get channel/detector assignement
try:
dn = np.array(dfd.get_value('detector_to_use').split(','), dtype=int)
except:
dn = np.array([int(dfd.get_value('detector_to_use'))])
channel_number = B.get_data(df, 'ch')
detector_id = B.get_data(df, 'detector_id')
ch_touse = channel_number[np.in1d(detector_id, dn)]
# flux grid
try:
flux_data_file = pf.get_value('flux_data_file')
except:
flux_data_file = 'flux.data'
print('using : ', flux_data_file, ' for flux and Em data')
# flux limiter
try:
flux_limiter_file = pf.get_value('flux_limiter_file')
except:
flux_limiter_file = 'flux_limit.data'
print('using : ', flux_limiter_file, ' for flux limit data')
# plot n-flux at mid-plane
try:
flux_data_file_mp = pf.get_value('flux_data_file_mp')
except:
flux_data_file_mp = None
orbit_output = open(output_dir + 'orbit_output').readlines()
# find the EQ file used:
eq_file = 'generic'
for d in orbit_output:
if (d.find('--> EQ File unit, name') >= 0.):
eq_file = d.split()[-1:][0]
# flux
print('reading flux data')
fl = gf.flux(output_dir + flux_data_file)
print('reading flux limit data')
fll_d = DF.dfile(output_dir + flux_limiter_file)
r_fll = np.array(fll_d.get_data('xlim'))
z_fll = np.array(fll_d.get_data('ylim'))
# limiter
print('reading limiter data')
li = gl.limiter(output_dir + 'limiter_drawing.data')
#orbits
print('reading orbits data')
# each view can now have several trajectories
PD_views = []
PD_views_f = []
PD_accept = []
PD_channel_number = []
PD_step = []
for i, i_d in enumerate(dn):
cc = ch_touse[i]
name_patt = output_dir + '/track_{}*.data'.format(i_d)
PD_view_files = G.glob(name_patt)
# use the first file in the list to get some parameters used for calculating rates
PDd = DF.pdfile(PD_view_files[0])
PD_accept.append(PDd.par.get_value('accept'))
PD_channel_number.append(
PDd.par.get_value('channel_number', var_type=int))
PD_step.append(PDd.par.get_value('stepsize'))
# load the trajectories for each view
PD_v = [vd.view(f) for f in PD_view_files]
PD_views_f.append(PD_view_files)
PD_views.append(PD_v)
print('channel : ', cc, ', detecor : ', i_d, ' loaded')
PD_accept = np.array(PD_accept)
#----------------------------------------------------------------------
# start drawing
#----------------------------------------------------------------------
draw_top_view = pf.get_value('draw_top_view', var_type=pf.Bool)
draw_top_view = True
if draw_top_view:
f1 = pl.figure(figsize=(11, 6))
# f1=pickle.load(file('neutron.pickle_both_view'))
else:
f1 = pl.gcf() #figure(figsize= (5,8))
#f1.text(0.1, 0.925, eq_file)
# draw 3 regions
if draw_top_view:
li.draw_all()
else:
li.draw_side_all()
# draw the rel. flux
# get a nice set of contour lines
# select the first plot
Em_cont = None
# axes = li.ax1.get_axes()
# f1.sca( axes )
axes = li.ax1
f1.sca(axes)
# draw the flux limit
pl.plot(r_fll, z_fll, color='m', linewidth=2.)
if plot_em:
Em_range = fl.Em.max() - fl.Em.min()
Em_min = fl.Em.min() + Em_range / 100.
v = np.linspace(Em_min, fl.Em.max() * cont_scale, ncont)
if em_filled:
Em_cont = fl.draw_Em_filled(v, cmap=colormap)
else:
Em_cont = fl.draw_Em(v)
if plot_psirel:
v = np.linspace(-0.1, fl.Zrel.max(), 23)
if psirel_filled:
fl.draw_psirel_filled(v, cmap=colormap)
else:
fl.draw_psirel(v)
# make a nice x-axis
axes.xaxis.set_major_locator(MaxNLocator(4))
#----------------------------------------------------------------------
# draw orbits
#----------------------------------------------------------------------
# # animation part
# for i, PDv in enumerate(PD_views):
# icol = dn[i]-1
# animate(li, PDv, color = colors[icol])
#
# axes = li.ax1.get_axes()
axes = li.ax1
f1.sca(axes)
for i, PDv in enumerate(PD_views):
icol = dn[i] - 1
plot_view_side(PDv, color=colors[icol], label='Ch {0:d}'.format(dn[i]))
#pl.legend(fontsize = 12,loc = 'upper left')
pl.title
# draw orbits into the top view
#draw_top_view=True
if draw_top_view:
# axes = li.ax2.get_axes()
axes = li.ax2
f1.sca(axes)
# draw a few orbits
for i, PDv in enumerate(PD_views):
icol = dn[i] - 1
plot_view_top(PDv,
color=colors[icol],
label='Ch {0:d}'.format(dn[i]))
# get the mid-plane emmissivity
if plot_em:
if (flux_data_file_mp != None):
# load data file
d = np.load(output_dir + '/' + flux_data_file_mp)
X = d['X']
Y = d['Y']
Em_mid = d['EM_mp']
Em_range = Em_mid.max() - Em_mid.min()
Em_min = Em_mid.min() + Em_range / 100.
v = np.linspace(Em_min, Em_mid.max() * cont_scale, ncont)
if em_filled:
Em_cont = pl.contourf(X, Y, Em_mid, v, cmap=colormap)
else:
Em_cont = pl.contour(X, Y, Em_mid, v, cmap=colormap)
#pl.legend(fontsize = 12, loc = 'upper left')
# The following code plots histogram of orbits midplane intersection radii
# h_range =(0.0, 0.3)#(0.6, 1.6)
# r0 = []
# f2 = pl.figure()
# for i,PDv in enumerate( PD_views ):
# icol = dn[i]-1
# rr = []
# for v in PDv:
# rr.append(get_effective_dist(v))#get_zero_crossing(v))
#
# rr = np.array(rr)
# r = rr.mean()
# h = B.histo(rr, range =h_range, bins = 200)
# h.plot(color = colors[icol])
# print colors[icol]
# sig_r = np.sqrt(rr.var())
# r0.append([h, r, sig_r, rr])
# # all done
# pl.xlabel('R (m)')
# pl.ylabel('counts')
# pl.title('mid-plane Radius')
#
# #pl.savefig(orbit_dir+'image.png')
pl.show()
def main(control_file):
# open control file and read parameters
c_file = control_file
cd = PF.pfile(c_file)
nml_dir = cd.get_value('input_dir')
nml_filename = cd.get_value('input_file')
make_new_nml = cd.get_value('make_new_nml', var_type=cd.Bool)
static_dir = cd.get_value('static_dir')
stat_file = cd.get_value('static_file')
dynamic_dir = cd.get_value('dynamic_dir')
dyn_file = cd.get_value('dynamic_file')
orbit_command = cd.get_value('orbit_command') + ' ' + c_file
# plot_command = cd.get_value('plot_command') + ' ' + c_file
##########################Obtaining Parameters and Data########################
# Grabbing dynamic data file
dd = B.get_file(dynamic_dir + dyn_file)
dpar = dd.par
# which detectors are used in the calculations
try:
det_use = np.array(dpar.get_value('detector_to_use').split(','),
dtype=int)
except:
det_use = np.array([int(dpar.get_value('detector_to_use'))])
# total number of detectors to be used in calculations
detectors = len(det_use)
# get the assigned detectors ids
detector_id = B.get_data(dd, 'detector_id')
# total number of detectors in dynamic file
N_det = len(detector_id)
# get the assigned channel numbers
channel_number = B.get_data(dd, 'ch')
# Port angle of each detector when the Reciprocating probe arm is at a rotation angle of 0, convert to rads
ppb = B.get_data(dd, 'phi_port_base') * dtr
# Theta angle of each detector when the Reciprocating
# probe arm is at a rotation angle of 0
# Port angle was input in degrees
tpb = B.get_data(dd, 'theta_port_base') * dtr
# Horizontal offset, from the center of the diagnostic, of each detector
# Horizontal offset was input in mm
dyo = B.get_data(dd, 'detector_horizontal_offset') * mm2m
# Radial offset of each detector (measured from the base)
# Radial offset was input in mm
dro = B.get_data(dd, 'detector_radial_axis_offset') * mm2m
# Height offset of each detector (measured from the center)
# Height offset was input in mm
dzo = B.get_data(dd, 'detector_height_offest') * mm2m
# detector type (Probe or Fixed)
det_type = B.get_data(dd, 'det_type')
# Alpha is the rotational angle of the RP arm
# converted to radians
alpha = dpar.get_value('RP_rotation') * dtr
##################################Making Calculations##########################
# indexes of fixed detectors
fixed_dets = np.where(det_type == 'Fixed')
# calculation of positions change for each Probe detector due to rotation
dyor = np.sqrt(dyo**2 + dzo**2) * np.cos(alpha + pol_angle(dyo, dzo))
dzor = np.sqrt(dyo**2 + dzo**2) * np.sin(alpha + pol_angle(dyo, dzo))
# RDist is the distance from the center of the tokamak to each detector (m)
RDist = np.sqrt((dpar.get_value('RDist') + dro +
dpar.get_value('RDist_offset'))**2 + dyor**2)
RDist[fixed_dets] = dro[fixed_dets]
# ZDist here is the height of each detector relative to the centr of the
# tokamak, in dynamic file ZDist is RP position hight
ZDist = dpar.get_value('ZDist') + dzor
ZDist[fixed_dets] = dzor[fixed_dets]
#RP phd angle
RP_phd = dpar.get_value('PHDangle')
# PHD angle shift for each detector relative to RP_phd
dphd = np.arcsin(dyor / RDist) / dtr
# phdangle is the toroidal angle of each detector in radians
phdangle = RP_phd + dphd
phdangle[fixed_dets] = dyo[fixed_dets] / mm2m
# The following are the calculations for the change in phi and theta angles
phi_port, theta_port = rotate_det(ppb, tpb, alpha, dphd * dtr)
phi_port /= dtr
theta_port /= dtr
phi_port[fixed_dets] = ppb[fixed_dets] / dtr
theta_port[fixed_dets] = tpb[fixed_dets] / dtr
#######################Detector orientation vectors for SolidWorks##############
# output_folder = '../MAST-U_output/g29975_TRANSP/DetectorsVectors/'
# vlen = 0.1 #vector lenght in meters
# for k in range(N_det):
# geom = open(output_folder + 'track' + str(k)+ '.dat', 'w+')
#
# xx=RDist[k]*np.cos(phdangle[k]*dtr)
# yy=RDist[k]*np.sin(phdangle[k]*dtr)
# zz=ZDist[k]
#
# geom.write('{} {} {}\n'.format(xx,yy,zz))
#
# print xx, yy, zz
#
# vx = -vlen*np.cos(phi_port[k]*dtr)*np.sin(theta_port[k]*dtr)
# vy = -vlen*np.sin(phi_port[k]*dtr)
# vz = vlen*np.cos(phi_port[k]*dtr)*np.cos(theta_port[k]*dtr)
#
# #print "V", vx, vy, vz
#
# v1 = vx*np.cos(phdangle[k]*dtr) - vy*np.sin(phdangle[k]*dtr)
# v2 = vx*np.sin(phdangle[k]*dtr) + vy*np.cos(phdangle[k]*dtr)
# v3 = vz
#
# #print "Vr", v1,v2,v3
# xx = xx + v1
# yy = yy + v2
# zz = zz + v3
#
# print xx, yy, zz
# geom.write('{} {} {}\n'.format(xx,yy,zz))
# geom.close()
#########################Creating New Dictionary###############################
# Physical Parameter Dictionary
PA = {
'PHDangle': phdangle,
'RDist': RDist,
'phi_port': phi_port,
'theta_port': theta_port,
'channel_number': channel_number,
'detector_id': detector_id,
'ZDist': ZDist,
'detector_number': det_use,
'detectors': detectors
}
PAK = list(PA.keys())
PAG = PA.get
# ######################Make a new NML file#########################
if make_new_nml is True:
staticf = open(static_dir + stat_file, 'r').readlines()
# opens and reads static file
staticf = [s.replace('\r\n', '\n') for s in staticf]
#this is for linux compatibility
bothf = open(nml_dir + nml_filename, 'w+')
# creates nml writable file
# Writing New nml file
bothf.writelines(staticf[:staticf.index(' &orbit_par\n') + 1])
# writes the static file into the new nml file
# Selecting the inputs under orbitpar
orbit_par = [
'detectors', 'detector_number', 'detector_id', 'channel_number',
'theta_port', 'phi_port'
]
# Writing Parameters into orbit_par in nml file
for i in orbit_par:
for k in range(N_det):
try:
bothf.write(' ' + i + '({0:1})'.format(k + 1) +
'= {0:1}\n'.format(PAG(i)[k]))
except:
if i == 'detector_number': break
bothf.write(' ' + i + '= {0:1}\n'.format(PAG(i)))
break
bothf.write('\n')
bothf.writelines(staticf[staticf.index(' &orbit_par\n') +
1:staticf.index(' &detection\n') + 1])
# Choosing keys for detection nml section
detection = []
for i in PAK:
if i not in orbit_par:
detection.append(i)
# Writing Parameters into detection in nml file
for i in detection:
for k in range(N_det):
try:
bothf.write(' ' + i + '({0:1})'.format(k + 1) +
'= {0:1}\n'.format(PAG(i)[k]))
except:
bothf.write(' ' + i + '= {0:1}\n'.format(PAG(i)))
break
bothf.write('\n')
bothf.writelines(staticf[staticf.index(' &detection\n') + 1:])
bothf.close()
os.system(orbit_command)