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Commit 99257257 authored by Yngve Levinsen's avatar Yngve Levinsen
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flake8 passing for lib_tw 

a lot of blank except: were replaced,
maybe some of them incorrectly
parent 9519c704
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Stage: deploy
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ess/lib_tw.py
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− 111
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......@@ -13,7 +13,7 @@ from __future__ import print_function
import numpy
from struct import pack
from struct import pack, unpack
from itertools import chain
from subprocess import check_output
......@@ -204,16 +204,16 @@ class LATTICE:
if self.lst[k].apt is not None:
self.lst[i].apt = self.lst[k].apt
break
except:
except IndexError:
pass
else:
for k in range(i)[::-1]:
try:
self.lst[i].apt = self.lst[k].apt
break
except:
except IndexError:
pass
except:
except IndexError:
pass
def update_gamma(self):
......@@ -225,7 +225,7 @@ class LATTICE:
self.lst[i].gamma = self.lst[i - 1].gamma
try:
self.lst[i].update_gamma()
except:
except IndexError:
pass
def update_st(self, file_name):
......@@ -278,7 +278,7 @@ class LATTICE:
if i == "ERROR" and lin[0] == "BEAM":
continue
settings = {}
for j in xrange(len(lin[2:]) / 3):
for j in range(len(lin[2:]) / 3):
k = int(lin[2 + 3 * j])
val = float(lin[4 + 3 * j])
if k in settings:
......@@ -414,13 +414,13 @@ class PROJECT:
def exe(self):
opt_exe = "TraceWin64_noX11 " + self.file_name_proj
if self.file_name_lat != None:
if self.file_name_lat is not None:
opt_exe += " dat_file=" + self.file_name_lat
if self.path_cal != None:
if self.path_cal is not None:
opt_exe += " path_cal=" + self.path_cal
if self.seed != None:
if self.seed is not None:
opt_exe += " random_seed=" + self.seed
if self.flag_hide != None:
if self.flag_hide is not None:
opt_exe += " hide"
# if self.path_cal!=None:
......@@ -435,20 +435,19 @@ class PROJECT:
class PARTRAN:
"""
Note:
- The list not complete. Add parameters as needed.
History:
- 2016.02.17: Changed how to identify the line of indices.
- 2016.02.17: Added a logic to avoid #/0 for LEBT.
"""
def __init__(self, file_name):
# Consts to convert phs to z.
mass = 938.272029
c = 2.99792458
freq = 352.21
......@@ -515,13 +514,13 @@ class PARTRAN:
# Way around for 0 emitt
for i in range(len(self.s)):
if self.epsx[i] == 0.0:
self.epsx[i] = inf
self.epsx[i] = numpy.inf
if self.epsy[i] == 0.0:
self.epsy[i] = inf
self.epsy[i] = numpy.inf
if self.epsz[i] == 0.0:
self.epsz[i] = inf
self.epsz[i] = numpy.inf
if self.epsp[i] == 0.0:
self.epsp[i] = inf
self.epsp[i] = numpy.inf
# Additional instances
self.gamma = data[idx_gamma] + 1.0
......@@ -538,13 +537,13 @@ class PARTRAN:
# Set inf emitt back to 0
for i in range(len(self.s)):
if self.epsx[i] == inf:
if self.epsx[i] == numpy.inf:
self.epsx[i] = 0.0
if self.epsy[i] == inf:
if self.epsy[i] == numpy.inf:
self.epsy[i] = 0.0
if self.epsz[i] == inf:
if self.epsz[i] == numpy.inf:
self.epsz[i] = 0.0
if self.epsp[i] == inf:
if self.epsp[i] == numpy.inf:
self.epsp[i] = 0.0
# Convert to list (not necessary?)
......@@ -602,11 +601,11 @@ class DST:
# Read the file
with open(file_name) as file:
dummy = numpy.fromfile(file, dtype=numpy.uint8, count=2)
numpy.fromfile(file, dtype=numpy.uint8, count=2)
Nptcl = numpy.fromfile(file, dtype=numpy.uint32, count=1)[0]
Ibeam = numpy.fromfile(file, dtype=numpy.float64, count=1)[0]
freq = numpy.fromfile(file, dtype=numpy.float64, count=1)[0]
dummy = numpy.fromfile(file, dtype=numpy.uint8, count=1)
numpy.fromfile(file, dtype=numpy.uint8, count=1)
x = (
numpy.fromfile(file, dtype=numpy.float64, count=Nptcl * 6)
.reshape(Nptcl, 6)
......@@ -656,11 +655,11 @@ class DENSITY:
Nelem : loss_num_(..), loss_pow_(..)
Nelem x Nstep: den
- History:
* 2015.11.12: Baseline ver
* 2016.03.29: Adapted to ver 9 (apt includes shifts)
* 2016.03.29: Adapted to ver 9 (apt includes shifts)
"""
def __init__(self, file_name):
......@@ -702,32 +701,48 @@ class DENSITY:
while True:
try:
# Partran and envelope
ver, year, flag_long = fromfile(file, dtype=uint16, count=3)
Nrun = fromfile(file, dtype=uint32, count=1)[0]
idx_elem.append(fromfile(file, dtype=uint32, count=1)[0])
Ibeam.append(fromfile(file, dtype=float32, count=1)[0])
s.append(fromfile(file, dtype=float32, count=1)[0])
ver, year, flag_long = numpy.fromfile(
file, dtype=numpy.uint16, count=3
)
Nrun = numpy.fromfile(file, dtype=numpy.uint32, count=1)[0]
idx_elem.append(
numpy.fromfile(file, dtype=numpy.uint32, count=1)[0]
)
Ibeam.append(numpy.fromfile(file, dtype=numpy.float32, count=1)[0])
s.append(numpy.fromfile(file, dtype=numpy.float32, count=1)[0])
if ver >= 9:
apt.append(fromfile(file, dtype=float32, count=4))
apt.append(numpy.fromfile(file, dtype=numpy.float32, count=4))
else:
apt.append(fromfile(file, dtype=float32, count=2))
Nstep = fromfile(file, dtype=uint32, count=1)[0]
cent_ave.append(fromfile(file, dtype=float32, count=7))
cent_rms.append(fromfile(file, dtype=float32, count=7))
xmax.append(fromfile(file, dtype=float32, count=7))
xmin.append(fromfile(file, dtype=float32, count=7))
apt.append(numpy.fromfile(file, dtype=numpy.float32, count=2))
Nstep = numpy.fromfile(file, dtype=numpy.uint32, count=1)[0]
cent_ave.append(numpy.fromfile(file, dtype=numpy.float32, count=7))
cent_rms.append(numpy.fromfile(file, dtype=numpy.float32, count=7))
xmax.append(numpy.fromfile(file, dtype=numpy.float32, count=7))
xmin.append(numpy.fromfile(file, dtype=numpy.float32, count=7))
if ver > 5:
sig_ave.append(fromfile(file, dtype=float32, count=7))
sig_rms.append(fromfile(file, dtype=float32, count=7))
sig_ave.append(
numpy.fromfile(file, dtype=numpy.float32, count=7)
)
sig_rms.append(
numpy.fromfile(file, dtype=numpy.float32, count=7)
)
if ver >= 6:
cent_min.append(fromfile(file, dtype=float32, count=7))
cent_max.append(fromfile(file, dtype=float32, count=7))
cent_min.append(
numpy.fromfile(file, dtype=numpy.float32, count=7)
)
cent_max.append(
numpy.fromfile(file, dtype=numpy.float32, count=7)
)
if ver >= 7:
eps_ave.append(fromfile(file, dtype=float32, count=3))
eps_rms.append(fromfile(file, dtype=float32, count=3))
eps_ave.append(
numpy.fromfile(file, dtype=numpy.float32, count=3)
)
eps_rms.append(
numpy.fromfile(file, dtype=numpy.float32, count=3)
)
if ver >= 8:
accpt.append(fromfile(file, dtype=float32, count=3))
Nptcl.append(fromfile(file, dtype=uint64, count=1)[0])
accpt.append(numpy.fromfile(file, dtype=numpy.float32, count=3))
Nptcl.append(numpy.fromfile(file, dtype=numpy.uint64, count=1)[0])
# Partran only
if Nptcl[-1] > 0:
loss_num.append([])
......@@ -736,56 +751,74 @@ class DENSITY:
den_pow.append([])
for n in range(Nrun):
loss_num[-1].append(
fromfile(file, dtype=uint64, count=1)[0]
numpy.fromfile(file, dtype=numpy.uint64, count=1)[0]
)
loss_pow[-1].append(
fromfile(file, dtype=float32, count=1)[0]
numpy.fromfile(file, dtype=numpy.float32, count=1)[0]
)
loss_num_ave.append(sum(loss_num[-1]))
loss_num_rms.append(fromfile(file, dtype=uint64, count=1)[0])
loss_num_min.append(fromfile(file, dtype=uint64, count=1)[0])
loss_num_max.append(fromfile(file, dtype=uint64, count=1)[0])
loss_num_rms.append(
numpy.fromfile(file, dtype=numpy.uint64, count=1)[0]
)
loss_num_min.append(
numpy.fromfile(file, dtype=numpy.uint64, count=1)[0]
)
loss_num_max.append(
numpy.fromfile(file, dtype=numpy.uint64, count=1)[0]
)
loss_pow_ave.append(sum(loss_pow[-1]))
loss_pow_rms.append(fromfile(file, dtype=float64, count=1)[0])
loss_pow_min.append(fromfile(file, dtype=float32, count=1)[0])
loss_pow_max.append(fromfile(file, dtype=float32, count=1)[0])
loss_pow_rms.append(
numpy.fromfile(file, dtype=numpy.float64, count=1)[0]
)
loss_pow_min.append(
numpy.fromfile(file, dtype=numpy.float32, count=1)[0]
)
loss_pow_max.append(
numpy.fromfile(file, dtype=numpy.float32, count=1)[0]
)
for k in range(7):
if flag_long == 1:
den[-1].append(
fromfile(file, dtype=uint64, count=Nstep)
numpy.fromfile(
file, dtype=numpy.uint64, count=Nstep
)
)
else:
den[-1].append(
fromfile(file, dtype=uint32, count=Nstep)
numpy.fromfile(
file, dtype=numpy.uint32, count=Nstep
)
)
if Ibeam[-1] > 0:
for k in range(3):
den_pow[-1].append(
fromfile(file, dtype=float32, count=Nstep)
numpy.fromfile(
file, dtype=numpy.float32, count=Nstep
)
)
# print Nrun,Nptcl[-1],idx_elem[-1] # Diag
except:
except IndexError:
break
# -- Reshape arrays
apt = swapaxes(apt, 1, 0)
accpt = swapaxes(accpt, 1, 0)
cent_ave = swapaxes(cent_ave, 1, 0)
cent_rms = swapaxes(cent_rms, 1, 0)
cent_max = swapaxes(cent_max, 1, 0)
cent_min = swapaxes(cent_min, 1, 0)
sig_ave = swapaxes(sig_ave, 1, 0)
sig_rms = swapaxes(sig_rms, 1, 0)
eps_ave = swapaxes(eps_ave, 1, 0)
eps_rms = swapaxes(eps_rms, 1, 0)
xmax = swapaxes(xmax, 1, 0)
xmin = swapaxes(xmin, 1, 0)
apt = numpy.swapaxes(apt, 1, 0)
accpt = numpy.swapaxes(accpt, 1, 0)
cent_ave = numpy.swapaxes(cent_ave, 1, 0)
cent_rms = numpy.swapaxes(cent_rms, 1, 0)
cent_max = numpy.swapaxes(cent_max, 1, 0)
cent_min = numpy.swapaxes(cent_min, 1, 0)
sig_ave = numpy.swapaxes(sig_ave, 1, 0)
sig_rms = numpy.swapaxes(sig_rms, 1, 0)
eps_ave = numpy.swapaxes(eps_ave, 1, 0)
eps_rms = numpy.swapaxes(eps_rms, 1, 0)
xmax = numpy.swapaxes(xmax, 1, 0)
xmin = numpy.swapaxes(xmin, 1, 0)
if Nptcl[0] > 0:
loss_num = swapaxes(loss_num, 1, 0)
loss_pow = swapaxes(loss_pow, 1, 0)
den = swapaxes(den, 1, 0)
den_pow = swapaxes(den_pow, 1, 0)
loss_num = numpy.swapaxes(loss_num, 1, 0)
loss_pow = numpy.swapaxes(loss_pow, 1, 0)
den = numpy.swapaxes(den, 1, 0)
den_pow = numpy.swapaxes(den_pow, 1, 0)
# -- Take care ave and rms
......@@ -819,21 +852,21 @@ class DENSITY:
# -- Define std (around to avoid sqrt(-eps))
if Nrun > 1:
cent_std = numpy.sqrt(around(cent_rms ** 2 - cent_ave ** 2, 12))
sig_std = numpy.sqrt(around(sig_rms ** 2 - sig_ave ** 2, 12))
eps_std = numpy.sqrt(around(eps_rms ** 2 - eps_ave ** 2, 12))
cent_std = nan_to_num(cent_std) # Replace nan with 0
sig_std = nan_to_num(sig_std) # Replace nan with 0
eps_std = nan_to_num(eps_std) # Replace nan with 0
cent_std = numpy.sqrt(numpy.around(cent_rms ** 2 - cent_ave ** 2, 12))
sig_std = numpy.sqrt(numpy.around(sig_rms ** 2 - sig_ave ** 2, 12))
eps_std = numpy.sqrt(numpy.around(eps_rms ** 2 - eps_ave ** 2, 12))
cent_std = numpy.nan_to_num(cent_std) # Replace nan with 0
sig_std = numpy.nan_to_num(sig_std) # Replace nan with 0
eps_std = numpy.nan_to_num(eps_std) # Replace nan with 0
if Nptcl[0] > 0:
loss_num_std = numpy.sqrt(
around(loss_num_rms ** 2 - loss_num_ave ** 2, 16)
numpy.around(loss_num_rms ** 2 - loss_num_ave ** 2, 16)
)
loss_pow_std = numpy.sqrt(
around(loss_pow_rms ** 2 - loss_pow_ave ** 2, 16)
numpy.around(loss_pow_rms ** 2 - loss_pow_ave ** 2, 16)
)
loss_num_std = nan_to_num(loss_num_std) # Replace nan with 0
loss_pow_std = nan_to_num(loss_pow_std) # Replace nan with 0
loss_num_std = numpy.nan_to_num(loss_num_std) # Replace nan with 0
loss_pow_std = numpy.nan_to_num(loss_pow_std) # Replace nan with 0
# -- Convert to list (just in case...)
......@@ -1000,7 +1033,7 @@ def plt2x(path_file):
x.append(
[[unpack("f", file.read(4))[0] for l in range(7)] for k in range(Nptcl)]
)
except:
except IndexError:
break
file.close()
......@@ -1054,8 +1087,8 @@ def x2twiss(x):
2015.07.30
"""
x = [x_i - mean(x_i) for x_i in numpy.array(x).transpose()]
sig = [[mean(x_i * x_k) for x_k in x] for x_i in x]
x = [x_i - numpy.mean(x_i) for x_i in numpy.array(x).transpose()]
sig = [[numpy.mean(x_i * x_k) for x_k in x] for x_i in x]
eps = [
numpy.sqrt(numpy.linalg.det(numpy.array(sig)[i : i + 2][:, i : i + 2]))
for i in (0, 2, 4)
......@@ -1130,7 +1163,7 @@ def loss_elem2den(s, loss, file_name_dt="", dlt_dt=5e-6):
len(L_dt), Ndt
)
)
except:
except FileNotFoundError:
pass
# Take care loss in 0 length elem
......@@ -1154,8 +1187,8 @@ def loss_elem2den(s, loss, file_name_dt="", dlt_dt=5e-6):
sys.exit()
# Define L
l = [s[i + 1] - s[i] for i in range(len(s) - 1)]
l.insert(0, 0.0)
lngth = [s[i + 1] - s[i] for i in range(len(s) - 1)]
lngth.insert(0, 0.0)
# L=[s[i+1]-s[i] for i in range(len(s)-1)]; L.insert(0,0.0)
# Take care DTL part if "file_name_dt" is given
......@@ -1167,11 +1200,11 @@ def loss_elem2den(s, loss, file_name_dt="", dlt_dt=5e-6):
).transpose()[:2]
# Replace cell lengths with DT lengths
Ndt = 0
for i in range(len(l)):
dl = list(abs(l_cell - l[i]))
for i in range(len(lngth)):
dl = list(abs(l_cell - lngth[i]))
dl_min = min(dl)
if dl_min < dlt_dt:
l[i] = l_dt[dl.index(dl_min)]
lngth[i] = l_dt[dl.index(dl_min)]
Ndt += 1
# Check
if Ndt != len(l_cell):
......@@ -1180,18 +1213,18 @@ def loss_elem2den(s, loss, file_name_dt="", dlt_dt=5e-6):
len(l_cell), Ndt
)
)
except:
except FileNotFoundError:
pass
# Take care inf loss den
for i in range(len(l)):
if l[i] == 0.0 and loss[i] != 0.0:
for i in range(len(lngth)):
if lngth[i] == 0.0 and loss[i] != 0.0:
if i == 1:
print("The 1st elem has 0 length and yet has a loss, exiting...")
sys.exit()
else:
k = 1
while l[i - k] == 0.0:
while lngth[i - k] == 0.0:
k += 1
loss[i - k] += loss[i]
loss[i] = 0.0
......@@ -1199,11 +1232,11 @@ def loss_elem2den(s, loss, file_name_dt="", dlt_dt=5e-6):
# Finally, convert to loss density
loss_den = []
for i in range(len(l)):
for i in range(len(lngth)):
if loss[i] == 0.0:
loss_den.append(0.0)
else:
loss_den.append(loss[i] / l[i])
loss_den.append(loss[i] / lngth[i])
return loss_den
......@@ -1427,16 +1460,16 @@ def _update_field_map_dict(dictionary, folder_path):
# with open(path_file) as file:
# while True:
# try:
# ver=fromfile(file,dtype=uint16,count=3)[0] # version, year, vlong
# Nelem.append(fromfile(file,dtype=uint32,count=2)[1]) # Nrun, Nelem
# s.append(fromfile(file,dtype=float32,count=4)[1]) # Ibeam, s, aptx, apty
# fromfile(file,dtype=uint32,count=1) # Nslice ??
# x.append(list(fromfile(file,dtype=float32,count=7*4)[:2])) # ave & etc
# if ver>=5: fromfile(file,dtype=float32,count=7*2) # ver >= 5 part
# if ver>=6: fromfile(file,dtype=float32,count=7*2) # ver >= 6 part
# if ver>=7: fromfile(file,dtype=float32,count=3*2) # ver >= 7 part
# if ver>=8: fromfile(file,dtype=float32,count=1*3) # ver >= 8 part
# fromfile(file,dtype=uint64,count=1) # Nptcl
# ver=fromfile(file,dtype = numpy.uint16,count=3)[0] # version, year, vlong
# Nelem.append( numpy.fromfile(file,dtype = numpy.uint32,count=2)[1]) # Nrun, Nelem
# s.append( numpy.fromfile(file,dtype = numpy.float32,count=4)[1]) # Ibeam, s, aptx, apty
# numpy.fromfile(file,dtype = numpy.uint32,count=1) # Nslice ??
# x.append(list( numpy.fromfile(file,dtype = numpy.float32,count=7*4)[:2])) # ave & etc
# if ver>=5: numpy.fromfile(file,dtype = numpy.float32,count=7*2) # ver >= 5 part
# if ver>=6: numpy.fromfile(file,dtype = numpy.float32,count=7*2) # ver >= 6 part
# if ver>=7: numpy.fromfile(file,dtype = numpy.float32,count=3*2) # ver >= 7 part
# if ver>=8: numpy.fromfile(file,dtype = numpy.float32,count=1*3) # ver >= 8 part
# numpy.fromfile(file,dtype = numpy.uint64,count=1) # Nptcl
# except:
# break
......
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