def dist_wrap(l1, l2, norm_index=2):
""" return the average distance modulo 2pi between two lists of angles
The average is calculated as an n-norm.
>>> round(dist_wrap([2, 1, 0], [-4, 1, 3]), 7)
3.013336
"""
diffs = modtwopi(np.array(l1) - np.array(l2), offset=0)
return np.linalg.norm(diffs, norm_index)
def plot_array_phase(freq, ax=plt.gca(), fixp=False, ref_probe=0, ref_offset=0):
""" Warning - this really should have FS passed as an arg
Also, to fix 2Pi skips - if there are a number of noisy graphs that
should be similar. Choose the 2pi skip that keeps a graph closest to
an already processed one (or the ensemble average?) (how??)
"""
if not isinstance(freq, int): # convert reals to the corresponding index
findex = np.argsort(np.abs(freqs - freq))[0]
print('freq {freq} index {findex}'.format(**locals())),
else:
findex = freq
phaselist_orig = [np.angle(FTs[isig][findex]) for isig in isigs]
phaselist = np.copy(phaselist_orig) # save the original for debugging
phaselist = fix2pi_skips(phaselist) if fixp else phaselist
phaselist = phaselist - phaselist[ref_probe] if ref_probe > -999 else phaselist
if (ref_probe) > -999 and (not fixp): # use mod2pi to
phaselist = modtwopi(phaselist, offset=ref_offset)
ax.plot(phaselist, label=str('{f:.1f}kHz'.format(f=freqs[findex]/1e3)))
ax.legend(fontsize='xx-small', loc='best',ncol=1 + min(3, len(isigs)//6))
plt.show(block=0)
def dists(a, instances, mask = None, method='euler'):
""" calculate the RMS (not RSS) distance of the phase set to all phase sets
based on std in new_mode_identify
presently takes 1.4 secs for 1Mx14 float32.(100ns/elt
4ns +,*, 21ns sqrt 43 ns modtwopi 26n (new fmod version)
"""
if (len(a) != np.shape(instances)[-1]):
raise ValueError('shape of phases does not match shape of sample')
if mask is None: mask=np.arange(len(a))
if not(hasattr(instances, 'std')):
print('make phase_array into an np array to speed up 100x')
# the following assumes it is a structured array - it may be a list~!~
instances = np.array(instances.tolist())
cc = np.tile(a[mask], (np.shape(instances)[0],1))
# next line is a little faster
# x=sum(modtwopi((phases[:,sel]-subset[clinds[cl][0]]),offset=0)**2,1)
#
# time x=sqrt(average(modtwopi((phases[0:1000000].astype(float32)+1)**2),1))
# float32 should be faster than float or float16 (worst) but
# because subset is float32, it is promoted to that precision automatically
sq = (modtwopi(instances[:,mask]-a, offset=0))**2
return(np.sqrt(np.average(sq,len(np.shape(instances))-1)))
def fsplot_phase(input_data, closed=True, ax=None, hold=0, offset=0, block=False):
""" plot the phase of a flucstruc, optionally inserting the first point
at the end (if closed=True). Applies to closed arrays (e.g complete 2pi).
Until Feb 2013, this version did not yet attempt to take into account angles, or check
that adjacent channels are adjacent (i.e. ch2-ch1, ch2-c2 etc).
Channel names are taken from the fs and plotted abbreviated
1/1/2011: TODO This appears to work only for database = None config
1/17/2011: bdb: May be fixed - I had used channel instead of channel.name
"""
# extract by channels
ch1n,ch2n,ch21n,dp = [],[],[],[]
# bdb this line should be replaced by a call to a routine names something
#like <plotted_width> to help in deciding if the label will fit on the
#current graph.
if ax is None: ax=pl.gca()
# why is this repeated below
max_chars = get_axes_pixcells(ax)[2]/8 # assuming an 10 pt font is 8 wide.
if (2*len(input_data.dphase)
*(2+len(input_data.dphase[0].channel_1.name)))> max_chars:
sep = '\n-'
else: sep = '-'
#sep = '-'
# 2013 change order from ch1-ch2 to ch2-ch1 = ch2 - ch1
for dpn in input_data.dphase:
ch1n.append(dpn.channel_1.name)
ch2n.append(dpn.channel_2.name)
ch21n.append(dpn.channel_2.name+sep+dpn.channel_1.name)
dp.append(dpn.delta)
min_length = max(1,40/len(input_data.channels))
# min_length - min_length???
short_names_1,p,s = split_names(ch1n, min_length=2) # need to break up loops to do this
short_names_2,p,s = split_names(ch2n, min_length=5) #
# need to know how big the shortened names are before deciding on the separator
if (2*len(input_data.dphase)*(2+len(short_names_1[0])))> max_chars:
sep = '\n-'
else: sep = '-'
ch21n = [ch2n[i]+sep+ch1n[i] for i in range(len(ch1n))]
short_ch21n = [short_names_2[i]+sep+short_names_1[i]
for i in range(len(short_names_1))]
# correct result for a diag that doesn MP1,2,3,4,5,6,1, and not closed
#ch21n = ['MP2-MP1', 'MP3-MP2', 'MP4-MP3', 'MP5-MP4', 'MP6-MP5', 'MP1-MP6']
# if closed, and only 1-6 in the file, want the same!
if closed: # ch2 will be MP1, ch1 will be MP6 MP1-MP6
ch1n.append(ch2n[-1])
ch2n.append(ch1n[0])
ch21n.append(ch2n[-1]+sep+ch1n[0])
short_ch21n.append(short_names_2[-1]+sep+short_names_1[0])
#dp.insert(0,dp[-1])
# closed means use the phase diff from the ends
# sign bug fixed here - made closed opposite sign to open..
dp=np.append(dp,modtwopi(-np.sum(dp),offset=offset))
#dp = fix2pi_skips(dp, around=offset)
dp = modtwopi(dp, offset=offset)
if hold == 0: ax.clear()
# This is a kludgy way to read coordinates. Should be through acquisition.base or acquisition.'device'
Phi = np.array([2*np.pi/360*float(pyfusion.config.get
('Diagnostic:{cn}'.
format(cn=c.name),
'Coords_reduced')
.split(',')[0])
for c in input_data.channels])
Theta = np.array([2*np.pi/360*float(pyfusion.config.get
('Diagnostic:{cn}'.
format(cn=c.name),
'Coords_reduced')
.split(',')[1])
for c in input_data.channels])
if closed:
Phi = np.append(Phi, Phi[0])
Theta = np.append(Theta, Theta[0])
if len(np.unique(Theta)) > 1:
AngName = 'Theta'
Ang = Theta
dAngfor1 = np.pi/13 #dAngfor1 is the average coil dph for M=1
span = (np.pi)/13 # span is the average coil spacing in radians
else:
AngName = 'Phi'
Ang = Phi
dAngfor1 = (2*np.pi)/6
span = 2*np.pi/6
# expect Phi from ~.2 to twopi+.2 (if closed)
Angfix = fix2pi_skips(Ang,around=3.5)
# Here use fix2pi_skips, as we want the coil location angle to
# increase monotonically - the raw numbers in .cfg may not start at zero
# need to make sure the right dp is divided by the right dPhi!
ax.plot(fix2pi_skips(Angfix[0:-1],around=np.pi),dp/np.diff(Angfix)*span,
'+-',label='dp/d'+AngName[0])
ax.plot(fix2pi_skips(Angfix[0:-1],around=np.pi),dp,'o-', label='d'+AngName)
ax.set_xlim([ax.get_xlim()[0],
ax.get_xlim()[1]+np.average(np.diff(Angfix))])
ax.plot(ax.get_xlim(),[0,0],':k',linewidth=0.5)
for N in (-3,-2,-1,1,2,3): ax.plot(ax.get_xlim(),[N*dAngfor1,N*dAngfor1],':r',linewidth=0.5)
tot=np.sum(dp)
over = Angfix[-1] - Angfix[0]
print(tot)
if closed: # only makes sense to draw a mean dp line if closed
ax.plot(ax.get_xlim(),[tot/(2*np.pi),tot/(2*np.pi)],':b',linewidth=0.5)
ax.legend(prop=FontProperties(size='small'))
ax.set_title('sum = {s:.2f} over {o:.2f} ~ {r:.1f}'
.format(s=tot,o=over, r=tot/over))
debug_(pyfusion.DEBUG, 1, key='fs_phase')
#ax.set_xticks(range(len(dp)))
ax.set_xticks(Angfix)
ax.set_xticklabels(short_ch21n)
pl.show(block=block)
from pyfusion.data.DA_datamining import DA
from pyfusion.acquisition.read_text_pyfusion import read_text_pyfusion, plot_fs_DA, merge_ds
from pyfusion.visual.window_manager import rmw, cmw, omw, lmw, smw
from pyfusion.utils.utils import fix2pi_skips, modtwopi
from pyfusion.visual.sp import off, on, tog
from pyfusion.data.convenience import between, bw, btw, decimate, his, broaden
dd=DA('W7X_MIR/DAMIRNOV_41_13_nocache_15_3m_2018fl.zip')
dd.info()
fig4, axs4=plt.subplots(4,1)
figfs, axf=plt.subplots(1,1)
plot_fs_DA(dd, ax=axf)
w6=where((btw(dd['freq'],4,8)) & (dd['amp']>0.0015) & (dd['t_mid']>3.2) &(dd['shot'] == 180904035))[0]
plot_fs_DA(dd, ax=axf, inds=w6,marker='s',ms=300,alpha=0.5)
axs4[0].plot(array([modtwopi(ph,offset=0) for ph in dd['phases'][w6]]).T,'c',lw=.5)
w6=where((btw(dd['freq'],4,8)) & (dd['amp']>0.015) & (dd['t_mid']>3.2) &(dd['shot'] == 180904035))[0]
axs4[0].plot(array([modtwopi(ph,offset=0) for ph in dd['phases'][w6]]).T,'b',lw=.5)
axs4[0].set_title('4-8kHz, after 3.2s')
w0=where((btw(dd['freq'],0,2)) & (dd['amp']>0.0015) & (dd['t_mid']>3.2) &(dd['shot'] == 180904035))[0]
plot_fs_DA(dd, ax=axf, inds=w0,marker='s',ms=300,alpha=0.5)
axs4[1].plot(array([modtwopi(ph,offset=0) for ph in dd['phases'][w0]]).T,'b',lw=.5)
axs4[1].set_title('0-2kHz, > 3.2s')
w6e=where((btw(dd['freq'],4,12)) & (dd['amp']>0.015) & (dd['t_mid']<3.2) &(dd['shot'] == 180904035))[0]
plot_fs_DA(dd, ax=axf, inds=w6e,marker='^',ms=300,alpha=0.5)
axs4[2].plot(array([modtwopi(ph,offset=0) for ph in dd['phases'][w6e]]).T,'c',lw=.5)
w6e=where((btw(dd['freq'],4,12)) & (dd['amp']>0.025) & (dd['t_mid']<3.2) &(dd['shot'] == 180904035))[0]
axs4[2].plot(array([modtwopi(ph,offset=0) for ph in dd['phases'][w6e]]).T,'b',lw=1)
axs4[2].set_title('4-12kHz, before 3.2s')
axs4[3].plot(array([modtwopi(ph,offset=.5) for ph in dd['phases']])[::5].T,'b',lw=.015)
axs4[3].set_title('all')
def dist2(a,b, method='euler'):
ax = (max(len(np.shape(a)),len(np.shape(b)))) - 1
return(np.sum((modtwopi((np.array(a)- np.array(b)),offset=0)**2),ax))
if DAfile != '':
da = DA(DAfile, load=1)
else:
print('try for a da in locals()')
try:
da
except NameError as reason:
print(' no da - did you use run -i?')
wh = da['indx'] # all of them
#wh = np.where((btw(da['freq'],2,4)) & (da['amp']>0.012) )[0]
wh = np.where(da['shot'] == 180904035)[0]
phs = da['phases'][wh].tolist()
inds = da['indx'][wh].tolist()
ctrs = np.mean(modtwopi(phs, 0), 0)
num = len(ctrs)
print(len(wh))
for left in range(len(phs), min_left, -1):
if version == 1:
ctrs = np.mean(modtwopi(phs, 0), 0)
dists = [dist_wrap(ctrs, phases) / num for phases in phs]
if np.max(dists) < tolerance:
break
worst = np.argmax(dists)
phs.pop(worst)
inds.pop(worst)
"""
worst = np.argsort(dists)[::-1] # this won't work as position in list changes....
def fsplot_phase(input_data,
closed=True,
ax=None,
hold=0,
offset=0,
AngName=None,
block=False):
""" plot the phase of a flucstruc, optionally inserting the first point
at the end (if closed=True). Applies to closed arrays (e.g complete 2pi).
Until Feb 2013, this version did not yet attempt to take into account angles, or check
that adjacent channels are adjacent (i.e. ch2-ch1, ch2-c2 etc).
Channel names are taken from the fs and plotted abbreviated
1/1/2011: TODO This appears to work only for database = None config
1/17/2011: bdb: May be fixed - I had used channel instead of channel.name
"""
# extract by channels
ch1n, ch2n, ch21n, dp = [], [], [], []
# bdb this line should be replaced by a call to a routine names something
#like <plotted_width> to help in deciding if the label will fit on the
#current graph.
if ax is None: ax = pl.gca()
# why is this repeated below
max_chars = get_axes_pixcells(
ax)[2] / 8 # assuming an 10 pt font is 8 wide.
if (2 * len(input_data.dphase) *
(2 + len(input_data.dphase[0].channel_1.name))) > max_chars:
sep = '\n-'
else:
sep = '-'
#sep = '-'
# 2013 change order from ch1-ch2 to ch2-ch1 = ch2 - ch1
for dpn in input_data.dphase:
ch1n.append(dpn.channel_1.name)
ch2n.append(dpn.channel_2.name)
ch21n.append(dpn.channel_2.name + sep + dpn.channel_1.name)
dp.append(dpn.delta)
min_length = max(1, 40 / len(input_data.channels))
# min_length - min_length???
short_names_1, p, s = split_names(
ch1n, min_length=2) # need to break up loops to do this
short_names_2, p, s = split_names(ch2n, min_length=4) # used to be 5
# need to know how big the shortened names are before deciding on the separator
if (2 * len(input_data.dphase) * (2 + len(short_names_1[0]))) > max_chars:
sep = '\n-'
else:
sep = '-'
ch21n = [ch2n[i] + sep + ch1n[i] for i in range(len(ch1n))]
short_ch21n = [
short_names_2[i] + sep + short_names_1[i]
for i in range(len(short_names_1))
]
# correct result for a diag that doesn MP1,2,3,4,5,6,1, and not closed
#ch21n = ['MP2-MP1', 'MP3-MP2', 'MP4-MP3', 'MP5-MP4', 'MP6-MP5', 'MP1-MP6']
# if closed, and only 1-6 in the file, want the same!
if closed: # ch2 will be MP1, ch1 will be MP6 MP1-MP6
ch1n.append(ch2n[-1])
ch2n.append(ch1n[0])
ch21n.append(ch2n[-1] + sep + ch1n[0])
short_ch21n.append(short_names_2[-1] + sep + short_names_1[0])
#dp.insert(0,dp[-1])
# closed means use the phase diff from the ends
# sign bug fixed here - made closed opposite sign to open..
dp = np.append(dp, modtwopi(-np.sum(dp), offset=offset))
#dp = fix2pi_skips(dp, around=offset)
dp = modtwopi(dp, offset=offset)
if hold == 0: ax.clear()
# This is a kludgey way to read coordinates. Should be through acquisition.base or acquisition.'device'
Phi = np.array([
2 * np.pi / 360 * float(
pyfusion.config.get('Diagnostic:{cn}'.format(cn=c.config_name),
'Coords_reduced').split(',')[0])
for c in input_data.channels
])
Theta = np.array([
2 * np.pi / 360 * float(
pyfusion.config.get('Diagnostic:{cn}'.format(cn=c.config_name),
'Coords_reduced').split(',')[1])
for c in input_data.channels
])
if closed:
Phi = np.append(Phi, Phi[0])
Theta = np.append(Theta, Theta[0])
# kludgey - needed to deal with Shaun's array - should
# really convert form cylindrical
if AngName is not 'Phi' and len(np.unique(Theta)) > 1:
AngName = 'Theta'
Ang = Theta
dAngformeq1 = np.pi / 13 #dAngformeq1 is the average coil dph for M=1
span = (np.pi) / 13 # span is the average coil spacing in radians
else:
AngName = 'Phi'
Ang = Phi
dAngformeq1 = (2 * np.pi) / 6 # seems hardwired for LHD or shaun??
span = 2 * np.pi / 6
if closed:
dAngformeq1 = (2 * np.pi) / len(Ang) # bdb 2019 - overide if closed
span = dAngformeq1 # why two veraible for the same thing - are they same?
# expect Phi from ~.2 to twopi+.2 (if closed)
Angfix = fix2pi_skips(Ang, around=3.5)
# Here use fix2pi_skips, as we want the coil location angle to
# increase monotonically - the raw numbers in .cfg may not start at zero
# need to make sure the right dp is divided by the right dPhi!
ax.plot(
fix2pi_skips(Angfix[0:-1], around=np.pi),
dp / np.diff(Angfix) * span,
'+-',
label='dp/d' + AngName[0],
lw=0.2,
)
ax.plot(fix2pi_skips(Angfix[0:-1], around=np.pi),
dp,
'o-',
label='d' + AngName)
ax.set_xlim(
[ax.get_xlim()[0],
ax.get_xlim()[1] + np.average(np.diff(Angfix))])
ax.plot(ax.get_xlim(), [0, 0], ':k', linewidth=0.5)
for N in (-3, -2, -1, 1, 2, 3):
ax.plot(ax.get_xlim(), [N * dAngformeq1, N * dAngformeq1],
':m',
linewidth=0.2,
label=['', '~dth(m=1)'][N == 1])
tot = np.sum(dp)
over = Angfix[-1] - Angfix[0]
print(tot)
if closed: # only makes sense to draw a mean dp line if closed
ax.plot(ax.get_xlim(), [tot / (2 * np.pi), tot / (2 * np.pi)],
':b',
linewidth=0.5)
ax.legend(prop=FontProperties(size='xx-small'))
ax.set_title('sum = {s:.2f} over {o:.2f} ~ {r:.1f}'.format(s=tot,
o=over,
r=tot / over))
debug_(pyfusion.DEBUG, 1, key='fs_phase')
#ax.set_xticks(range(len(dp)))
ax.set_xticks(Angfix)
# think this out better - e.g. this 128 should be adjusted according to max_chars
ax.set_xticklabels(short_ch21n,
fontsize=min(128 // len(short_ch21n), 10),
rotation=['horizontal', 'vertical'][len(Angfix) > 8])
print('block = ', block)
pl.show(block=block)
