diff --git a/scripts/Calibration/Examples/TubeCalibDemoMerlin.py b/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
index 10e0381418697434df6cc57d3627945f23bc5a0c..aa7eeabfd432d0662121e4e3d01ecad45ab71ac4 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
@@ -149,11 +149,11 @@ def calibrateMerlin(filename):
CalibratedComponent = ['MERLIN/door3/tube_1_%d' % (i) for i in range(1, 9)]
half_diff_center = (
- 2.92713867188 - 1.22879882813) / 2 # difference among the expected center position for both tubes
-
- # here a little bit of attempts is necessary. The efective center position and lengh is different for the calibrated tube, that
- # is the reason, the calibrated values of the smaller tube does not seems aligned with the others. By, finding the 'best' half_diff_center
- # value, the alignment occurs nicely.
+ 2.92713867188 - 1.22879882813) / 2 # difference among the expected center position for
+ # both tubes here a little bit of attempts is necessary.
+ # The effective center position and lengh is different for the calibrated tube, that is the reason,
+ # the calibrated values of the smaller tube does not seems aligned with the others. By, finding the
+ # 'best' half_diff_center value, the alignment occurs nicely.
half_diff_center = 0.835 #
# the knownpositions were given with the center of the bigger tube as origin, to convert
diff --git a/scripts/DiamondAttenuationCorrection/FitTrans.py b/scripts/DiamondAttenuationCorrection/FitTrans.py
index e18aeebdae721a3b435c6f046bc4b3b1968f57f2..a7c2495e90d3df47909645bbc60ffe6649bd016d 100644
--- a/scripts/DiamondAttenuationCorrection/FitTrans.py
+++ b/scripts/DiamondAttenuationCorrection/FitTrans.py
@@ -59,8 +59,8 @@ def calcDspacing(a, b, c, alp, bet, gam, h, k, l):
sb = np.sin(np.radians(bet))
sg = np.sin(np.radians(gam))
- oneoverdsq = (1.0 - ca**2 - cb**2 - cg**2 + 2 * ca * cb * cg)**(-1) * \
- ((h * sa / a)**2 + (k * sb / b)**2 + (l * sg / c)**2
+ oneoverdsq = (1.0 - ca ** 2 - cb ** 2 - cg ** 2 + 2 * ca * cb * cg) ** (-1) * \
+ ((h * sa / a) ** 2 + (k * sb / b) ** 2 + (l * sg / c) ** 2
+ (2 * k * l / (b * c)) * (cb * cg - ca) + (2 * l * h / (c * a)) * (cg * ca - cb)
+ (2 * h * k / (a * b)) * (ca * cb - cg))
@@ -121,22 +121,22 @@ def forbidden(h, k, l):
result = 0
# condition 1
- if ((h != 0)and (k != 0) and (l != 0)): # general hkl
+ if ((h != 0) and (k != 0) and (l != 0)): # general hkl
term1 = h + k
term2 = h + l # all have to be even
term3 = k + l
- if not((term1 % 2) == 0 and (term2 % 2) == 0 and (term3 % 2) == 0):
+ if not ((term1 % 2) == 0 and (term2 % 2) == 0 and (term3 % 2) == 0):
result = 1
boolresult = bool(result)
return boolresult
else:
result = 0
- #% condition 2
+ # % condition 2
if ((h == 0) and (k != 0) and (l != 0)): # 0kl reflections
term1 = k + l
mod4 = mod(term1, 4)
- if not(mod4 == 0 and mod(k, 2) == 0 and mod(l, 2) == 0):
+ if not (mod4 == 0 and mod(k, 2) == 0 and mod(l, 2) == 0):
result = 1
boolresult = bool(result)
return boolresult
@@ -145,7 +145,7 @@ def forbidden(h, k, l):
# condition 3
if (h == k): # hhl reflections
- if not(mod(h + l, 2) == 0):
+ if not (mod(h + l, 2) == 0):
result = 1
boolresult = bool(result)
return boolresult
@@ -153,9 +153,9 @@ def forbidden(h, k, l):
result = 0
# condition 4
- if ((h == 0) and (k == 0) and (l != 0)): # 00l reflections not including 000
+ if ((h == 0) and (k == 0) and (l != 0)): # 00l reflections not including 000
mod4 = mod(l, 4)
- if not(mod4 == 0):
+ if not (mod4 == 0):
result = 1
boolresult = bool(result)
return boolresult
@@ -191,7 +191,7 @@ def allowedDiamRefs(hmin, hmax, kmin, kmax, lmin, lmax):
# create new array with all h!=0 k!=0 l!=0
hkl = np.zeros(shape=(0, 3))
for i in range(n):
- if not(allhkl[i][0] == 0 and allhkl[i][1] == 0 and allhkl[i][2] == 0):
+ if not (allhkl[i][0] == 0 and allhkl[i][1] == 0 and allhkl[i][2] == 0):
hkl = np.vstack((hkl, [allhkl[i][0], allhkl[i][1], allhkl[i][2]]))
d.append(calcDspacing(3.56683, 3.56683, 3.56683, 90,
90, 90, hkl[k][0], hkl[k][1], hkl[k][2]))
@@ -224,7 +224,7 @@ def getISAWub(fullfilename):
'''
fileID = fullfilename
if fileID == 1:
- print('Error opening file: ' + fullfilename)
+ print(('Error opening file: ' + fullfilename))
f = open(fileID, "r")
lines = f.readlines()
f.close()
@@ -236,8 +236,9 @@ def getISAWub(fullfilename):
UB[i][0], UB[i][1], UB[i][2] = lines[i].split()
UB = UB.transpose()
for i in range(3, 5):
- lattice[i - 3][0], lattice[i - 3][1], lattice[i - 3][2], lattice[i - 3][3], lattice[i - 3][4], lattice[i - 3][5], \
- non = lines[i].split()
+ lattice[i - 3][0], lattice[i - 3][1], lattice[i - 3][2], lattice[i - 3][3], lattice[i - 3][4], lattice[i - 3][
+ 5], \
+ non = lines[i].split()
print('Successfully got UB and lattice')
@@ -260,93 +261,93 @@ def pkintread(hkl, loc):
returns pkint = np. array - 1D vector
'''
- #A = np.genfromtxt('diamond_reflist.csv', delimiter=',', skip_header=True)
+ # A = np.genfromtxt('diamond_reflist.csv', delimiter=',', skip_header=True)
# print A
- A = np.array([[1.00000000e+00, 1.00000000e+00, 1.00000000e+00, 8.00000000e+00,
- 2.06110000e+00, 5.54000000e+04],
- [2.00000000e+00, 2.00000000e+00, 0.00000000e+00, 1.20000000e+01,
- 1.26220000e+00, 7.52000000e+04],
- [3.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 1.07640000e+00, 2.98000000e+04],
- [2.00000000e+00, 2.00000000e+00, 2.00000000e+00, 8.00000000e+00,
- 1.03060000e+00, 2.50000000e-25],
- [4.00000000e+00, 0.00000000e+00, 0.00000000e+00, 6.00000000e+00,
- 8.92500000e-01, 4.05000000e+04],
- [3.00000000e+00, 3.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 8.19000000e-01, 1.61000000e+04],
- [4.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 7.28700000e-01, 2.18000000e+04],
- [5.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 6.87000000e-01, 8.64000000e+03],
- [3.00000000e+00, 3.00000000e+00, 3.00000000e+00, 8.00000000e+00,
- 6.87000000e-01, 8.64000000e+03],
- [4.00000000e+00, 4.00000000e+00, 0.00000000e+00, 1.20000000e+01,
- 6.31100000e-01, 1.17000000e+04],
- [5.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
- 6.03400000e-01, 4.65000000e+03],
- [4.00000000e+00, 4.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 5.95000000e-01, 1.83000000e-12],
- [6.00000000e+00, 2.00000000e+00, 0.00000000e+00, 2.40000000e+01,
- 5.64500000e-01, 6.31000000e+03],
- [5.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
- 5.44400000e-01, 2.50000000e+03],
- [6.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 5.38200000e-01, 8.80000000e-26],
- [4.00000000e+00, 4.00000000e+00, 4.00000000e+00, 8.00000000e+00,
- 5.15300000e-01, 3.40000000e+03],
- [5.00000000e+00, 5.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 4.99900000e-01, 1.35000000e+03],
- [7.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 4.99900000e-01, 1.35000000e+03],
- [6.00000000e+00, 4.00000000e+00, 2.00000000e+00, 4.80000000e+01,
- 4.77100000e-01, 1.83000000e+03],
- [7.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
- 4.64800000e-01, 7.25000000e+02],
- [5.00000000e+00, 5.00000000e+00, 3.00000000e+00, 2.40000000e+01,
- 4.64800000e-01, 7.25000000e+02],
- [8.00000000e+00, 0.00000000e+00, 0.00000000e+00, 6.00000000e+00,
- 4.46200000e-01, 9.84000000e+02],
- [7.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
- 4.36100000e-01, 3.90000000e+02],
- [6.00000000e+00, 4.00000000e+00, 4.00000000e+00, 2.40000000e+01,
- 4.32900000e-01, 1.53000000e-13],
- [6.00000000e+00, 6.00000000e+00, 0.00000000e+00, 1.20000000e+01,
- 4.20700000e-01, 5.30000000e+02],
- [8.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 4.20700000e-01, 5.30000000e+02],
- [5.00000000e+00, 5.00000000e+00, 5.00000000e+00, 8.00000000e+00,
- 4.12200000e-01, 2.10000000e+02],
- [7.00000000e+00, 5.00000000e+00, 1.00000000e+00, 4.80000000e+01,
- 4.12200000e-01, 2.10000000e+02],
- [6.00000000e+00, 6.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 4.09500000e-01, 1.98000000e-26],
- [8.00000000e+00, 4.00000000e+00, 0.00000000e+00, 2.40000000e+01,
- 3.99100000e-01, 2.85000000e+02],
- [7.00000000e+00, 5.00000000e+00, 3.00000000e+00, 4.80000000e+01,
- 3.91900000e-01, 1.13000000e+02],
- [9.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 3.91900000e-01, 1.13000000e+02],
- [8.00000000e+00, 4.00000000e+00, 2.00000000e+00, 4.80000000e+01,
- 3.89500000e-01, 4.44000000e-14],
- [6.00000000e+00, 6.00000000e+00, 4.00000000e+00, 2.40000000e+01,
- 3.80600000e-01, 1.53000000e+02],
- [9.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
- 3.74200000e-01, 6.08000000e+01],
- [8.00000000e+00, 4.00000000e+00, 4.00000000e+00, 2.40000000e+01,
- 3.64400000e-01, 8.26000000e+01],
- [9.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
- 3.58800000e-01, 3.27000000e+01],
- [7.00000000e+00, 5.00000000e+00, 5.00000000e+00, 2.40000000e+01,
- 3.58800000e-01, 3.27000000e+01],
- [7.00000000e+00, 7.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 3.58800000e-01, 3.27000000e+01]])
+ A = np.array([[1.00000000e+00, 1.00000000e+00, 1.00000000e+00, 8.00000000e+00,
+ 2.06110000e+00, 5.54000000e+04],
+ [2.00000000e+00, 2.00000000e+00, 0.00000000e+00, 1.20000000e+01,
+ 1.26220000e+00, 7.52000000e+04],
+ [3.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 1.07640000e+00, 2.98000000e+04],
+ [2.00000000e+00, 2.00000000e+00, 2.00000000e+00, 8.00000000e+00,
+ 1.03060000e+00, 2.50000000e-25],
+ [4.00000000e+00, 0.00000000e+00, 0.00000000e+00, 6.00000000e+00,
+ 8.92500000e-01, 4.05000000e+04],
+ [3.00000000e+00, 3.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 8.19000000e-01, 1.61000000e+04],
+ [4.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 7.28700000e-01, 2.18000000e+04],
+ [5.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 6.87000000e-01, 8.64000000e+03],
+ [3.00000000e+00, 3.00000000e+00, 3.00000000e+00, 8.00000000e+00,
+ 6.87000000e-01, 8.64000000e+03],
+ [4.00000000e+00, 4.00000000e+00, 0.00000000e+00, 1.20000000e+01,
+ 6.31100000e-01, 1.17000000e+04],
+ [5.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
+ 6.03400000e-01, 4.65000000e+03],
+ [4.00000000e+00, 4.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 5.95000000e-01, 1.83000000e-12],
+ [6.00000000e+00, 2.00000000e+00, 0.00000000e+00, 2.40000000e+01,
+ 5.64500000e-01, 6.31000000e+03],
+ [5.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
+ 5.44400000e-01, 2.50000000e+03],
+ [6.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 5.38200000e-01, 8.80000000e-26],
+ [4.00000000e+00, 4.00000000e+00, 4.00000000e+00, 8.00000000e+00,
+ 5.15300000e-01, 3.40000000e+03],
+ [5.00000000e+00, 5.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 4.99900000e-01, 1.35000000e+03],
+ [7.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 4.99900000e-01, 1.35000000e+03],
+ [6.00000000e+00, 4.00000000e+00, 2.00000000e+00, 4.80000000e+01,
+ 4.77100000e-01, 1.83000000e+03],
+ [7.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
+ 4.64800000e-01, 7.25000000e+02],
+ [5.00000000e+00, 5.00000000e+00, 3.00000000e+00, 2.40000000e+01,
+ 4.64800000e-01, 7.25000000e+02],
+ [8.00000000e+00, 0.00000000e+00, 0.00000000e+00, 6.00000000e+00,
+ 4.46200000e-01, 9.84000000e+02],
+ [7.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
+ 4.36100000e-01, 3.90000000e+02],
+ [6.00000000e+00, 4.00000000e+00, 4.00000000e+00, 2.40000000e+01,
+ 4.32900000e-01, 1.53000000e-13],
+ [6.00000000e+00, 6.00000000e+00, 0.00000000e+00, 1.20000000e+01,
+ 4.20700000e-01, 5.30000000e+02],
+ [8.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 4.20700000e-01, 5.30000000e+02],
+ [5.00000000e+00, 5.00000000e+00, 5.00000000e+00, 8.00000000e+00,
+ 4.12200000e-01, 2.10000000e+02],
+ [7.00000000e+00, 5.00000000e+00, 1.00000000e+00, 4.80000000e+01,
+ 4.12200000e-01, 2.10000000e+02],
+ [6.00000000e+00, 6.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 4.09500000e-01, 1.98000000e-26],
+ [8.00000000e+00, 4.00000000e+00, 0.00000000e+00, 2.40000000e+01,
+ 3.99100000e-01, 2.85000000e+02],
+ [7.00000000e+00, 5.00000000e+00, 3.00000000e+00, 4.80000000e+01,
+ 3.91900000e-01, 1.13000000e+02],
+ [9.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 3.91900000e-01, 1.13000000e+02],
+ [8.00000000e+00, 4.00000000e+00, 2.00000000e+00, 4.80000000e+01,
+ 3.89500000e-01, 4.44000000e-14],
+ [6.00000000e+00, 6.00000000e+00, 4.00000000e+00, 2.40000000e+01,
+ 3.80600000e-01, 1.53000000e+02],
+ [9.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
+ 3.74200000e-01, 6.08000000e+01],
+ [8.00000000e+00, 4.00000000e+00, 4.00000000e+00, 2.40000000e+01,
+ 3.64400000e-01, 8.26000000e+01],
+ [9.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
+ 3.58800000e-01, 3.27000000e+01],
+ [7.00000000e+00, 5.00000000e+00, 5.00000000e+00, 2.40000000e+01,
+ 3.58800000e-01, 3.27000000e+01],
+ [7.00000000e+00, 7.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 3.58800000e-01, 3.27000000e+01]])
diamd = A[:, 4]
- #diamMult = A[:, 3] # unused variable
+ # diamMult = A[:, 3] # unused variable
diamFCalcSq = A[:, 5]
nref = hkl.shape[0]
- #% disp(['there are: ' num2str(nref) ' reflections']);
- #% whos loc
+ # % disp(['there are: ' num2str(nref) ' reflections']);
+ # % whos loc
'''
% [i,j] = size(x);
@@ -363,10 +364,10 @@ def pkintread(hkl, loc):
for i in range(nref):
if loc[i][0] > 0:
- #% satisfies Bragg condition (otherwise ignore)
+ # % satisfies Bragg condition (otherwise ignore)
Fsq = Fsqcalc(loc[i][1], diamd, diamFCalcSq)
- #% Fsq = 1;
- L = (np.sin(np.radians(loc[i][2] / 2.0)))**2 # Lorentz correction
+ # % Fsq = 1;
+ L = (np.sin(np.radians(loc[i][2] / 2.0))) ** 2 # Lorentz correction
R = 1.0 # %dipLam(i)^4; %reflectivity correction
A = 1.0 # %Absorption correction
Ecor = 1
@@ -393,7 +394,7 @@ def Fsqcalc(d, diamd, diamFCalcSq):
% global sf111 sf220 sf311 sf400 sf331
'''
- #n = len(diamd) # unused variable
+ # n = len(diamd) # unused variable
ref = d
dif = abs(diamd - ref)
i = dif.argmin(0) # i is index of diamd closest to d
@@ -496,7 +497,7 @@ def getMANTIDdat_keepbinning(csvfile):
y = []
e = []
if fid < 0:
- print('Error opening file: ' + csvfile)
+ print(('Error opening file: ' + csvfile))
for i in range(1, len(lines)):
a, b, c = lines[i].split(",")
x.append(float(a))
@@ -534,7 +535,7 @@ def findeqvs(hkl):
nperm = len(permcomphkl)
for k in range(nperm):
if refhkl[0] == permcomphkl[k][0] and refhkl[1] == permcomphkl[k][1] and \
- refhkl[2] == permcomphkl[k][2]:
+ refhkl[2] == permcomphkl[k][2]:
eqvlab[j] = lab
lab += 1
@@ -558,8 +559,8 @@ def showx3(x):
global neqv1, eqvlab1, neqv2, eqvlab2
global difa, function_verbose
- #nref1 = hkl1.shape[0] # % number of reflections to integrate over # unused variable
- #nref2 = hkl2.shape[0] # % number of reflections to integrate over # unused variable
+ # nref1 = hkl1.shape[0] # % number of reflections to integrate over # unused variable
+ # nref2 = hkl2.shape[0] # % number of reflections to integrate over # unused variable
# % returns array with same dim as input labelling equivs
eqvlab1, neqv1 = findeqvs(hkl1)
eqvlab2, neqv2 = findeqvs(hkl2)
@@ -569,7 +570,7 @@ def showx3(x):
pkmult2 = x[6 + neqv1:7 + neqv1 + neqv2 - 1]
sf = x[neqv1 + neqv2 + 7 - 1]
pkwid1 = x[neqv1 + neqv2 + 8 - 1]
- #bgd = x[neqv1 + neqv2 + 8 - 1:neqv1 + neqv2 + 9 + 2 - 1] # unused variable
+ # bgd = x[neqv1 + neqv2 + 8 - 1:neqv1 + neqv2 + 9 + 2 - 1] # unused variable
pkwid2 = x[neqv1 + neqv2 + 10]
# % if diamond intensities the same, allow single scale f
relsf = x[neqv1 + neqv2 + 11]
@@ -577,18 +578,18 @@ def showx3(x):
L2 = x[neqv1 + neqv2 + 13]
print('_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/\n')
- print('Setting angles diam {0} : \nalp {1} bet {2} gam {3} \n'.format(
- 1, setang1[0], setang1[1], setang1[2]))
- print('pkmult1: {0}\n'.format(pkmult1))
- print('Setting angles diam {0} : \nalp {1} bet {2} gam {3} \n'.format(
- 2, setang2[0], setang2[1], setang2[2]))
- print('pkmult2: {0}\n'.format(pkmult2))
- print('Scale factor: {0}\n'.format(sf))
- print('pkwid1: {0}\n'.format(pkwid1))
- print('pkwid2: {0}\n'.format(pkwid2))
- print('Rel. scale factor : {0}\n'.format(relsf))
- print('Lambda multiplier: {0}\n'.format(delam))
- print('L2 sample to detector: {0} m\n'.format(L2))
+ print(('Setting angles diam {0} : \nalp {1} bet {2} gam {3} \n'.format(
+ 1, setang1[0], setang1[1], setang1[2])))
+ print(('pkmult1: {0}\n'.format(pkmult1)))
+ print(('Setting angles diam {0} : \nalp {1} bet {2} gam {3} \n'.format(
+ 2, setang2[0], setang2[1], setang2[2])))
+ print(('pkmult2: {0}\n'.format(pkmult2)))
+ print(('Scale factor: {0}\n'.format(sf)))
+ print(('pkwid1: {0}\n'.format(pkwid1)))
+ print(('pkwid2: {0}\n'.format(pkwid2)))
+ print(('Rel. scale factor : {0}\n'.format(relsf)))
+ print(('Lambda multiplier: {0}\n'.format(delam)))
+ print(('L2 sample to detector: {0} m\n'.format(L2)))
print('_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/\n')
@@ -646,7 +647,7 @@ def SimTransOutput3(name, x):
delam = x[neqv1 + neqv2 + 12]
L2 = x[neqv1 + neqv2 + 13]
- shftlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF**2)
+ shftlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF ** 2)
# number of lambda points to calculate over
npt = shftlam.shape[0]
# calculate information for peaks for crystal 1 using hkl,UB1, setang,
@@ -672,9 +673,9 @@ def SimTransOutput3(name, x):
# calculate background profile by multiplying this with coefficients
# themselves
bgdprof = nonzerobgd.dot(X)
- #bgdprof = np.outer(nonzerobgd, X)
+ # bgdprof = np.outer(nonzerobgd, X)
# print bgdprof
- #bgdprof = bgdprof[0, :]
+ # bgdprof = bgdprof[0, :]
# calculate peaks for crystal 1
t1 = np.zeros(npt) # initialise array containing profile
@@ -682,10 +683,10 @@ def SimTransOutput3(name, x):
if pktype == 1:
pkpars1[i][0] = pkpars1[i][0] * delam # linear lambda shift
sig = pkwid1 * pkpars1[i][0] + pkwid2 * \
- (pkpars1[i][0]**2.) # const del(lambda)/lambda
- extScl = pkpars1[i][0]**0 # lambda dependent extinction effect
+ (pkpars1[i][0] ** 2.) # const del(lambda)/lambda
+ extScl = pkpars1[i][0] ** 0 # lambda dependent extinction effect
t1 = t1 - extScl * pkmult1[int(eqvlab1[i])] * pkcalcint1[i] * (
- np.exp(-((shftlam - pkpars1[i][0])**2.) / (2 * (sig**2))))
+ np.exp(-((shftlam - pkpars1[i][0]) ** 2.) / (2 * (sig ** 2))))
# calculate peaks for crystal 2
t2 = np.zeros(npt) # initialise array containing profile
@@ -693,26 +694,26 @@ def SimTransOutput3(name, x):
if pktype == 1:
pkpars2[i][0] = pkpars2[i][0] * delam # linear lambda shift
sig = pkwid1 * pkpars2[i][0] + pkwid2 * \
- (pkpars2[i][0]**2.) # const del(lambda)/lambda
- extScl = pkpars2[i][0]**0 # lambda dependent extinction effect
+ (pkpars2[i][0] ** 2.) # const del(lambda)/lambda
+ extScl = pkpars2[i][0] ** 0 # lambda dependent extinction effect
t2 = t2 - extScl * pkmult2[int(eqvlab2[i])] * pkcalcint2[i] * (
- np.exp(-(shftlam - pkpars2[i][0])**2. / (2 * (sig**2))))
+ np.exp(-(shftlam - pkpars2[i][0]) ** 2. / (2 * (sig ** 2))))
# calculate final profile
ttot = (bgdprof + sf * t1) * (bgdprof + sf * t2)
- #t1 = 1.0;
+ # t1 = 1.0;
# t2 = 1.0;
# introduce weighting function and calc chi2...
w = np.ones(len(shftlam)) # equal weighting everywhere
- #i1 = np.where(shftlam > 2.15)[0][0]
- #j1 = np.where(shftlam > 2.65)[0][0]
+ # i1 = np.where(shftlam > 2.15)[0][0]
+ # j1 = np.where(shftlam > 2.65)[0][0]
# w[i1:j1] = 5 #extra weighting in region of first peaks
# i1 = find(lam>1.68,1,'first');
# j1 = find(lam>2.05,1,'first');
# w(i1:j1)=5; %extra weighting but not too much
resid = (y - ttot) * w
- chi2 = np.sum(resid**2. / (2 * e**2)) / npt
+ chi2 = np.sum(resid ** 2. / (2 * e ** 2)) / npt
output = 1
if output == 1:
@@ -810,7 +811,7 @@ def SimTrans3(x):
delam = x[neqv1 + neqv2 + 12]
L2 = x[neqv1 + neqv2 + 13]
- shftlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF**2)
+ shftlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF ** 2)
# number of lambda points to calculate over
npt = shftlam.shape[0]
# calculate information for peaks for crystal 1 using hkl,UB1, setang,
@@ -836,9 +837,9 @@ def SimTrans3(x):
# calculate background profile by multiplying this with coefficients
# themselves
bgdprof = nonzerobgd.dot(X)
- #bgdprof = np.outer(nonzerobgd, X)
+ # bgdprof = np.outer(nonzerobgd, X)
# print bgdprof
- #bgdprof = bgdprof[0, :]
+ # bgdprof = bgdprof[0, :]
# calculate peaks for crystal 1
t1 = np.zeros(npt) # initialise array containing profile
@@ -846,10 +847,10 @@ def SimTrans3(x):
if pktype == 1:
pkpars1[i][0] = pkpars1[i][0] * delam # linear lambda shift
sig = pkwid1 * pkpars1[i][0] + pkwid2 * \
- (pkpars1[i][0]**2.) # const del(lambda)/lambda
- extScl = pkpars1[i][0]**0 # lambda dependent extinction effect
+ (pkpars1[i][0] ** 2.) # const del(lambda)/lambda
+ extScl = pkpars1[i][0] ** 0 # lambda dependent extinction effect
t1 = t1 - extScl * pkmult1[int(eqvlab1[i])] * pkcalcint1[i] * (
- np.exp(-((shftlam - pkpars1[i][0])**2.) / (2 * (sig**2))))
+ np.exp(-((shftlam - pkpars1[i][0]) ** 2.) / (2 * (sig ** 2))))
# calculate peaks for crystal 2
t2 = np.zeros(npt) # initialise array containing profile
@@ -857,30 +858,30 @@ def SimTrans3(x):
if pktype == 1:
pkpars2[i][0] = pkpars2[i][0] * delam # linear lambda shift
sig = pkwid1 * pkpars2[i][0] + pkwid2 * \
- (pkpars2[i][0]**2.) # const del(lambda)/lambda
- extScl = pkpars2[i][0]**0 # lambda dependent extinction effect
+ (pkpars2[i][0] ** 2.) # const del(lambda)/lambda
+ extScl = pkpars2[i][0] ** 0 # lambda dependent extinction effect
t2 = t2 - extScl * pkmult2[int(eqvlab2[i])] * pkcalcint2[i] * (
- np.exp(-(shftlam - pkpars2[i][0])**2. / (2 * (sig**2))))
+ np.exp(-(shftlam - pkpars2[i][0]) ** 2. / (2 * (sig ** 2))))
# calculate final profile
ttot = (bgdprof + sf * t1) * (bgdprof + sf * t2)
- #t1 = 1.0;
+ # t1 = 1.0;
# t2 = 1.0;
# introduce weighting function and calc chi2...
w = np.ones(len(shftlam)) # equal weighting everywhere
- #i1 = np.where(shftlam > 2.15)[0][0]
- #j1 = np.where(shftlam > 2.65)[0][0]
+ # i1 = np.where(shftlam > 2.15)[0][0]
+ # j1 = np.where(shftlam > 2.65)[0][0]
# w[i1:j1] = 5 #extra weighting in region of first peaks
# i1 = find(lam>1.68,1,'first');
# j1 = find(lam>2.05,1,'first');
# w(i1:j1)=5; %extra weighting but not too much
resid = (y - ttot) * w
- chi2 = np.sum(resid**2. / (2 * e**2)) / npt
+ chi2 = np.sum(resid ** 2. / (2 * e ** 2)) / npt
# Print if the user wants verbose minimization
if function_verbose == 'y':
- print('Chi^2 ... ' + str(chi2))
+ print(('Chi^2 ... ' + str(chi2)))
return chi2
@@ -921,10 +922,10 @@ def FitTrans():
print('*diamonds allowed to have different dip intensities!*')
if cnstang == 1:
- print(
- '*Diam {0} setting angles constrained to range of +/- {1} about their current values*'.format(1, anglim1))
- print(
- '*Diam {0} setting angles constrained to range of +/- {1} about their current values*'.format(2, anglim2))
+ print((
+ '*Diam {0} setting angles constrained to range of +/- {1} about their current values*'.format(1, anglim1)))
+ print((
+ '*Diam {0} setting angles constrained to range of +/- {1} about their current values*'.format(2, anglim2)))
else:
print('no constraint on setting angles')
@@ -932,13 +933,13 @@ def FitTrans():
print('*intensity multipliers fixed*')
# Get Input Files...
- peaks_file = str(raw_input('Name of file containing diamond peaks: '))
+ peaks_file = str(input('Name of file containing diamond peaks: '))
- run_number = str(raw_input('Input run number for transmission data: '))
+ run_number = str(input('Input run number for transmission data: '))
# Build input filenames
- #fullfilename_ub1 = str(run_number) + 'UB1.dat' # unused variable
- #fullfilename_ub2 = str(run_number) + 'UB2.dat' # unused variable
+ # fullfilename_ub1 = str(run_number) + 'UB1.dat' # unused variable
+ # fullfilename_ub2 = str(run_number) + 'UB2.dat' # unused variable
fullfilename_trans = 'transNorm' + str(run_number) + '.dat'
# get both UB's
@@ -948,13 +949,13 @@ def FitTrans():
# uigetfile('*.dat','Choose UB matrix for upstream diamond:');
# fullfilename = [pathname filename];
# fullfilename_ub1 = 'snap13108UB1.dat'
- #UB1, remainder = getISAWub(fullfilename_ub1)
+ # UB1, remainder = getISAWub(fullfilename_ub1)
# [filename pathname ~] = ...
# uigetfile('*.dat','Choose UB matrix for downstream diamond:');
# fullfilename = [pathname filename];
# fullfilename_ub2 = 'snap13108UB2.dat'
- #UB2, remainder = getISAWub(fullfilename_ub2)
+ # UB2, remainder = getISAWub(fullfilename_ub2)
# get transmission data...
# [filename,pathname,~] = ...
@@ -963,7 +964,7 @@ def FitTrans():
fullfilename_trans = 'transNorm13148.csv'
TOF, yin, ein = getMANTIDdat_keepbinning(fullfilename_trans)
- print('Starting refinement for: ' + fullfilename_trans)
+ print(('Starting refinement for: ' + fullfilename_trans))
# set-up simulation
@@ -982,8 +983,8 @@ def FitTrans():
# rebin transmission data
lam = 0.0039558 * TOF / (L1 + initL2)
- print('wavelength limits: ' +
- str(lam[0]) + ' and ' + str(lam[len(lam) - 1]))
+ print(('wavelength limits: ' +
+ str(lam[0]) + ' and ' + str(lam[len(lam) - 1])))
minlam = 0.8
maxlam = 3.5
imin = np.where(lam >= minlam)[0][0]
@@ -1009,7 +1010,7 @@ def FitTrans():
# initial conditions for crystal 2
setang2 = np.zeros(3)
- #setang2[1:3][0] = 0.0
+ # setang2[1:3][0] = 0.0
a, b, c = pkposcalc(allhkl, UB2, setang2)
pkpars2 = np.column_stack((a, b, c))
@@ -1034,8 +1035,8 @@ def FitTrans():
hkl2 = np.vstack([hkl2, allhkl[i]])
k2 += 1
- print('There are: ' + str(k1) + ' expected dips due to Crystal 1')
- print('There are: ' + str(k2) + ' expected dips due to Crystal 2')
+ print(('There are: ' + str(k1) + ' expected dips due to Crystal 1'))
+ print(('There are: ' + str(k2) + ' expected dips due to Crystal 2'))
# determine equivalents
# returns array with same dim as input labelling equivs
@@ -1058,7 +1059,7 @@ def FitTrans():
pkcalcint2 *= 1e-6
pkmult2 = np.ones(neqv2) # peak intensity multiplier
- relsf = 1.0 # default value
+ relsf = 1.0 # default value
delam = 1.0
L2 = initL2
tbgd = bgd
@@ -1066,29 +1067,29 @@ def FitTrans():
# Either generate, or read variable array from file
# This is one big array with all the parameters to be refined in it.
- prevf = str(raw_input('Look for pars from a previous run ([y]/n)? '))
+ prevf = str(input('Look for pars from a previous run ([y]/n)? '))
if prevf == 'n':
x0 = np.hstack((setang1, pkmult1, setang2, pkmult2, sf,
pkwid, tbgd, pkwid2, relsf, delam, L2))
else:
- # choose which file to use
- parfilename = str(raw_input('Choose file with starting pars: '))
+ # choose which file to use
+ parfilename = str(input('Choose file with starting pars: '))
parfullfilename = parfilename
x0 = dlmread(parfullfilename)
- tog = str(raw_input('Got parameters from: \n' +
- parfilename + '\nUse these ([y]/n)?'))
+ tog = str(input('Got parameters from: \n' +
+ parfilename + '\nUse these ([y]/n)?'))
if tog == 'n':
x0 = np.hstack((setang1, pkmult1, setang2, pkmult2,
sf, pkwid, tbgd, pkwid2, relsf, delam, L2))
print('discarding pars from previous run')
- print(str(len(x0)) + ' parameters will be refined')
+ print((str(len(x0)) + ' parameters will be refined'))
nvar = len(x0)
- print('number of variables: ' + str(nvar))
- #nref1 = hkl1.shape[0] # unused variable
- #nref2 = hkl2.shape[0] # unused variable
+ print(('number of variables: ' + str(nvar)))
+ # nref1 = hkl1.shape[0] # unused variable
+ # nref2 = hkl2.shape[0] # unused variable
# need to apply correction in the case that pars from previous run had
# fxsamediam==1 and current run also has fxsamediam==1
@@ -1096,8 +1097,8 @@ def FitTrans():
if fxsamediam == 1 and x0[neqv1 + neqv2 + 11] != 1:
x0[6 + neqv1:7 + neqv1 + neqv2 - 1] = x0[3:4 +
- neqv2 - 1] / x0[neqv1 + neqv2 + 11]
- print('Diam 2 peak multipliers reset: ' + str(x0[neqv1 + neqv2 + 11]))
+ neqv2 - 1] / x0[neqv1 + neqv2 + 11]
+ print(('Diam 2 peak multipliers reset: ' + str(x0[neqv1 + neqv2 + 11])))
# check starting point
@@ -1113,7 +1114,7 @@ def FitTrans():
plt.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3,
ncol=3, mode="expand", borderaxespad=0.)
plt.show()
- print('Initial chi^2 is: ' + str(chi2))
+ print(('Initial chi^2 is: ' + str(chi2)))
showx3(x0)
@@ -1125,7 +1126,7 @@ def FitTrans():
A[3:4 + neqv1 - 1] = -1.0 # pkmult1 Contrains intensities to be positive
A[4 + neqv1 - 1:6 + neqv1] = 0.0 # setang2 *no constraint
A[6 + neqv1:7 + neqv1 + neqv2 - 1] = -1.0 # pkmult2
- A[6 + neqv1 + neqv2] = -1.0 # sf Scale factor must be +ve
+ A[6 + neqv1 + neqv2] = -1.0 # sf Scale factor must be +ve
A[7 + neqv1 + neqv2] = -1.0 # pkwid peak width must be +ve
A[neqv1 + neqv2 + 8:neqv1 + neqv2 + 9 + 2 - 1] = 0.0 # bgd *no constraint
A[(neqv1 + neqv2 + 10)] = 0.0 # *no constraint
@@ -1139,7 +1140,7 @@ def FitTrans():
Aeq[3:4 + neqv1 - 1] = 0.0 # pkmult1
Aeq[4 + neqv1 - 1:6 + neqv1] = 0.0 # setang2
Aeq[6 + neqv1:7 + neqv1 + neqv2 - 1] = 0.0 # pkmult2
- Aeq[6 + neqv1 + neqv2] = 0.0 # sf
+ Aeq[6 + neqv1 + neqv2] = 0.0 # sf
Aeq[7 + neqv1 + neqv2] = 0.0 # pkwid
Aeq[neqv1 + neqv2 + 8:neqv1 + neqv2 + 9 + 2 - 1] = 0 # unfixed bgd
Aeq[neqv1 + neqv2 + 10] = 0
@@ -1147,7 +1148,7 @@ def FitTrans():
Aeq[neqv1 + neqv2 + 12] = 0
Aeq[neqv1 + neqv2 + 13] = 0
- #beq = 0 # unused variable
+ # beq = 0 # unused variable
# lower bounds
lb = np.zeros(len(x0))
@@ -1155,7 +1156,7 @@ def FitTrans():
lb[3:4 + neqv1 - 1] = 0.5 # pkmult1
lb[4 + neqv1 - 1:6 + neqv1] = -10 # setang2
lb[6 + neqv1:7 + neqv1 + neqv2 - 1] = 0.5 # pkmult2
- lb[6 + neqv1 + neqv2] = 0.0 # sf
+ lb[6 + neqv1 + neqv2] = 0.0 # sf
lb[7 + neqv1 + neqv2] = 0.0005 # pkwid
lb[neqv1 + neqv2 + 8:neqv1 + neqv2 + 9 + 2 - 1] = [0.995, -0.0005] # bgd
lb[neqv1 + neqv2 + 10] = 0.5e-4 # 2nd order pkwid
@@ -1170,7 +1171,7 @@ def FitTrans():
ub[3:4 + neqv1 - 1] = 50 # pkmult1
ub[4 + neqv1 - 1:6 + neqv1] = 10 # setang2
ub[6 + neqv1:7 + neqv1 + neqv2 - 1] = 50 # pkmult2
- ub[6 + neqv1 + neqv2] = 50 # sf
+ ub[6 + neqv1 + neqv2] = 50 # sf
ub[7 + neqv1 + neqv2] = 0.01 # pkwid
ub[neqv1 + neqv2 + 8:neqv1 + neqv2 + 9 + 2 - 1] = [1.005, 0.0005] # bgd
ub[neqv1 + neqv2 + 10] = 1.0e-2 # 2nd order pkwid
@@ -1206,12 +1207,12 @@ def FitTrans():
ub[6 + neqv1:7 + neqv1 + neqv2 - 1] = x0[6 +
neqv1:7 + neqv1 + neqv2 - 1] + 0.01
- prompt = str(raw_input('Enter anything to begin refinement...'))
+ prompt = str(input('Enter anything to begin refinement...'))
print('Refining...\nMight take quite a long time...')
max_number_iterations = int(
- raw_input('Maximum number of iterations for minimization: '))
- function_verbose = str(raw_input('Verbose minimization ([y]/n): '))
+ input('Maximum number of iterations for minimization: '))
+ function_verbose = str(input('Verbose minimization ([y]/n): '))
# make dictionary holding constraints for minimization
# equalities (all must equal 0) and inequalities
@@ -1222,8 +1223,8 @@ def FitTrans():
# bounds have to be list of tuples with (lower, upper) for each parameter
bds = np.vstack((lb, ub)).T
- res = sp.minimize(SimTrans3, x0, method='SLSQP', bounds=bds, constraints=cons, options={'disp': True,
- 'maxiter': max_number_iterations})
+ res = sp.minimize(SimTrans3, x0, method='SLSQP', bounds=bds, constraints=cons,
+ options={'disp': True, 'maxiter': max_number_iterations})
# tolerance limits to put in minimization if you want so : 'ftol': 0.001
@@ -1245,9 +1246,9 @@ def FitTrans():
# neqv1+neqv2+11
# x[neqv1+neqv2+11]
x[6 + neqv1:7 + neqv1 + neqv2 - 1] = x[3:4 +
- neqv2 - 1] * x[neqv1 + neqv2 + 11]
- print('Diam 2 peak multipliers reset with factor: ' +
- str(x[neqv1 + neqv2 + 11]))
+ neqv2 - 1] * x[neqv1 + neqv2 + 11]
+ print(('Diam 2 peak multipliers reset with factor: ' +
+ str(x[neqv1 + neqv2 + 11])))
else:
# label ensuring I know that run did not use fxsamediam
x[neqv1 + neqv2 + 11] = 1.0
@@ -1261,13 +1262,13 @@ def FitTrans():
# calculate chi2 for best fit
chi2 = SimTrans3(x)
- print('Final Chi2 = ' + str(chi2))
+ print(('Final Chi2 = ' + str(chi2)))
# determine output wavelength range using refined L2 value
- #lamscale = x[neqv1 + neqv2 + 12] # unused variable
+ # lamscale = x[neqv1 + neqv2 + 12] # unused variable
L2 = x[neqv1 + neqv2 + 13]
- outlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF**2)
+ outlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF ** 2)
fig_name_final = 'Final result ' + run_number
plt.figure(fig_name_final)
@@ -1290,15 +1291,16 @@ def FitTrans():
plt.ylabel('Transmission')
plt.show()
- prompt = str(raw_input('output best fit to file ([y]/n): '))
+ prompt = str(input('output best fit to file ([y]/n): '))
if prompt == 'n':
print('Ending')
else:
fitparname = str(run_number) + '.best_fit_pars3.dat'
np.savetxt(fitparname, x, delimiter=',')
- print('output parameters written to file: \n' + fitparname)
+ print(('output parameters written to file: \n' + fitparname))
ofilename = str(run_number) + '.fitted3.dat'
SimTransOutput3(ofilename, x) # generate output file with fitted data
+
if __name__ == "__main__":
FitTrans()
diff --git a/scripts/HFIRPowderReduction/HfirPDReductionControl.py b/scripts/HFIRPowderReduction/HfirPDReductionControl.py
index 67fecc766589ab8b61168384299fcb1f7da2731d..e826905c598351da8115edb8f4b9f314c8d72ab0 100644
--- a/scripts/HFIRPowderReduction/HfirPDReductionControl.py
+++ b/scripts/HFIRPowderReduction/HfirPDReductionControl.py
@@ -6,7 +6,9 @@
#
############################################################################
import os
-import urllib.request, urllib.error, urllib.parse
+import urllib.request
+import urllib.error
+import urllib.parse
import math
import numpy
@@ -813,7 +815,7 @@ class HFIRPDRedControl(object):
if excludeddetlist is None:
excludeddetlist = []
else:
- print("[DB] Excluded detectors: %s" % (excludeddetlist), "Convert to numpy array", \
+ print("[DB] Excluded detectors: %s" % (excludeddetlist), "Convert to numpy array",
numpy.array(excludeddetlist))
basewsname = datamdws.name().split("_DataMD")[0]
diff --git a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
index 0c31eac4ba1e11b981b7705939718ba159305da5..51dba73f12d11e3603b7c712d59467a76a123bc1 100644
--- a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
+++ b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
@@ -621,13 +621,13 @@ class MantidConfigDirectInelastic(object):
if len(source) == 0:
raise ValueError(
'"replace" field of {0} file for instrument {1} has to contain attribute "var" and its value'
- .format(self._user_files_descr, self._user.instrument))
+ .format(self._user_files_descr, self._user.instrument))
# what should be placed instead of the replacement
dest = repl_info.getAttribute("by_var")
if len(dest) == 0:
raise ValueError(
'"replace" field of {0} file for instrument {1} has to contain attribute "by_var" and its value'
- .format(self._user_files_descr, self._user.instrument))
+ .format(self._user_files_descr, self._user.instrument))
# replace use-specific variables by their values
if '$' in dest:
diff --git a/scripts/Inelastic/Direct/PropertiesDescriptors.py b/scripts/Inelastic/Direct/PropertiesDescriptors.py
index b8aaad9d8e6a1666013bf468c57b90f2a52e0530..d20b7334118dbbbf038ce966a6bc86f83b281c11 100644
--- a/scripts/Inelastic/Direct/PropertiesDescriptors.py
+++ b/scripts/Inelastic/Direct/PropertiesDescriptors.py
@@ -10,7 +10,7 @@ import math
from collections import Iterable
import mantid.simpleapi as mantid
-from mantid import api, geometry, config
+from mantid import api
import Direct.ReductionHelpers as prop_helpers
import collections
@@ -663,9 +663,10 @@ class mon2NormalizationEnergyRange(PropDescriptor):
val1 = float(en_range[0])
if val1 < 0.1 or val1 > 0.9:
- message = "Lower mon2_norm_energy_range describes lower limit of energy to integrate neutron signal after the chopper.\n" \
- "The limit is defined as (this value)*incident_energy. Are you sure you want to set this_value to {0}?\n".format(
- val1)
+ message = "Lower mon2_norm_energy_range describes lower limit of energy to integrate neutron signal after" \
+ " the chopper.\nThe limit is defined as (this value)*incident_energy." \
+ " Are you sure you want to set this_value to {0}?\n".format(
+ val1)
if val1 > 1:
return (False, 2, message)
else:
@@ -673,9 +674,10 @@ class mon2NormalizationEnergyRange(PropDescriptor):
val2 = float(en_range[1])
if val2 < 1.1 or val2 > 1.9:
- message = "Upper mon2_norm_energy_range describes upper limit of energy to integrate neutron signal after the chopper.\n" \
- "The limit is defined as (this value)*incident_energy. Are you sure you want to set this_value to {0}?\n".format(
- val2)
+ message = "Upper mon2_norm_energy_range describes upper limit of energy to integrate neutron signal after" \
+ " the chopper.\nThe limit is defined as (this value)*incident_energy." \
+ " Are you sure you want to set this_value to {0}?\n".format(
+ val2)
if val2 > 1:
if result[0]:
result = (False, 1, message)
@@ -1050,7 +1052,9 @@ class MonovanIntegrationRange(prop_helpers.ComplexProperty):
value = result
if len(value) != 2:
raise KeyError("monovan_integr_range has to be list of two values, "
- "defining min/max values of integration range or None to use relative to incident energy limits")
+ "defining min/max values of integration range or None "
+ "to use relative to incident energy limits")
+
prop_helpers.ComplexProperty.__set__(self, tDict, value)
def validate(self, instance, owner):
@@ -1387,16 +1391,15 @@ class BackbgroundTestRange(PropDescriptor):
""" validate background test range """
test_range = self.__get__(instance, owner)
if test_range is None:
- return (True, 0, '')
+ return True, 0, ''
if test_range[0] >= test_range[1]:
- return (False, 2, ' Background test range: [{0}:{1}] is incorrect '.format(test_range[0], test_range[1]))
+ return False, 2, ' Background test range: [{0}:{1}] is incorrect '.format(test_range[0], test_range[1])
if test_range[0] < 0:
- return (
- False, 2, ' Background test range is TOF range, so it can not be negative={0}'.format(test_range[0]))
+ return False, 2, ' Background test range is TOF range, so it can not be negative={0}'.format(test_range[0])
if test_range[1] > 20000:
- return (False, 1, ' Background test range is TOF range, its max value looks suspiciously big={0}'.format(
- test_range[1]))
- return (True, 0, '')
+ return False, 1, ' Background test range is TOF range, its max value looks suspiciously big={0}'.format(
+ test_range[1])
+ return True, 0, ''
# end BackbgroundTestRange
diff --git a/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py b/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
index f21b87c61e6dff18176026764eb3d6e49aa482a9..1116c5b1cd9289691de4c4abf961b0012794f6fc 100644
--- a/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
+++ b/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
@@ -515,11 +515,7 @@ class BaseRefWidget(BaseWidget):
data_y = mantid.mtd[ws].dataY(0)
# cleanup data 0-> NAN
- for y_val in data_y:
- # print '-> data_y[j]: ' , data_y[j] , ' data_e[j]: ' , data_y[j]
- if y_val < 1e-12:
- _y_val = np.nan
-
+ data_y = [np.nan if y_val < 1e-12 else y_val for y_val in data_y]
_file_number += 1
# END OF DEBUGGING ONLY
diff --git a/scripts/MantidIPython/__init__.py b/scripts/MantidIPython/__init__.py
index 4ede76d88d070c30442eb2eeda0ed3d9098acbde..d5a758b524675515f6ed2fbb7741e2279c58559f 100644
--- a/scripts/MantidIPython/__init__.py
+++ b/scripts/MantidIPython/__init__.py
@@ -21,10 +21,8 @@
Some tools for use in ipython notebooks generated by Mantid.
"""
+# Suppress warnings about unused import as these
+# imports are important for iPython
from MantidIPython.plot_functions import *
-import warnings
-import mantid.kernel
-
-# Check if the version of Mantid being used matches the version which created the notebook.
-if "3.5.20160108.1509" != mantid.kernel.version_str():
- warnings.warn("Version of Mantid being used does not match version which created the notebook.")
+import warnings # noqa: F401
+import mantid.kernel # noqa: F401
diff --git a/scripts/reducer_singleton.py b/scripts/reducer_singleton.py
index c22114225429a55453059a77de500a956ae799e9..b0fdb5d7bc21e06a069041a3246466f3fe7cc738 100644
--- a/scripts/reducer_singleton.py
+++ b/scripts/reducer_singleton.py
@@ -1,8 +1,9 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
import random
import string
import os
import mantid
+import time
from isis_instrument import BaseInstrument
@@ -11,6 +12,7 @@ class ReductionStep(object):
"""
Base class for reduction steps
"""
+
@classmethod
def delete_workspaces(cls, workspace):
"""
@@ -25,8 +27,9 @@ class ReductionStep(object):
"""
Generate a unique name for an internal workspace
"""
- random_str = ''.join(random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
- return "__"+descriptor+"_"+extract_workspace_name(filepath)+"_"+random_str
+ random_str = ''.join(
+ random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
+ return "__" + descriptor + "_" + os.path.basename(filepath) + "_" + random_str
def execute(self, reducer, inputworkspace=None, outputworkspace=None):
"""
@@ -64,14 +67,16 @@ class Reducer(object):
output_workspaces = []
def __init__(self):
- self.UID = ''.join(random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
+ self.UID = ''.join(
+ random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
self._reduction_steps = []
def set_instrument(self, configuration):
if issubclass(configuration.__class__, BaseInstrument):
self.instrument = configuration
else:
- raise RuntimeError("Reducer.set_instrument expects an %s object, found %s" % (Instrument, configuration.__class__))
+ raise RuntimeError(
+ "Reducer.set_instrument expects an %s object, found %s" % (BaseInstrument, configuration.__class__))
def set_data_path(self, path):
"""
@@ -131,7 +136,7 @@ class Reducer(object):
self.pre_process()
# Go through the list of files to be reduced
- #for file_ws in self._data_files:
+ # for file_ws in self._data_files:
# for item in self._reduction_steps:
# try:
# result = item.execute(self, file_ws)
@@ -141,7 +146,7 @@ class Reducer(object):
# self.log_text += "\n%s\n" % sys.exc_value
# raise
- #any clean up, possibly removing workspaces
+ # any clean up, possibly removing workspaces
self.post_process()
# Determine which directory to use
@@ -152,8 +157,8 @@ class Reducer(object):
else:
output_dir = os.path.expanduser('~')
- self.log_text += "Reduction completed in %g sec\n" % (time.time()-t_0)
- log_path = os.path.join(output_dir,"%s_reduction.log" % instrument_name)
+ self.log_text += "Reduction completed in %g sec\n" % (time.time() - t_0)
+ log_path = os.path.join(output_dir, "%s_reduction.log" % instrument_name)
self.log_text += "Log saved to %s" % log_path
# Write the log to file
diff --git a/scripts/reduction/reducer.py b/scripts/reduction/reducer.py
index 383d3763fb79450591d1f73830240f50479aa017..0854667337f60305e66c3d5a3275ab5abea4e606 100644
--- a/scripts/reduction/reducer.py
+++ b/scripts/reduction/reducer.py
@@ -24,12 +24,11 @@ import os
import sys
import time
import types
+import uuid
from reduction.instrument import Instrument
-import mantid
-from mantid import simpleapi
+import mantid.simpleapi as mantid
import warnings
import inspect
-import random
from reduction.find_data import find_data
@@ -79,7 +78,7 @@ def validate_loader(func):
if data_file is None:
return
else:
- raise RuntimeError("SANSReductionSteps.LoadRun doesn't recognize workspace handle %s" % workspace)
+ raise RuntimeError("SANSReductionSteps.LoadRun doesn't recognize workspace handle %s" % inputworkspace)
else:
data_file = self._data_file
@@ -107,7 +106,7 @@ def validate_loader(func):
kwargs[kwargs["AlternateName"]] = data_file
self.algorithm = alg
- simpleapi.set_properties(alg, *(), **kwargs)
+ mantid.set_properties(alg, *(), **kwargs)
alg.execute()
if "OutputMessage" in propertyOrder:
return alg.getPropertyValue("OutputMessage")
@@ -146,7 +145,7 @@ def validate_loader(func):
if data_file is None:
return
else:
- raise RuntimeError("SANSReductionSteps.LoadRun doesn't recognize workspace handle %s" % workspace)
+ raise RuntimeError("SANSReductionSteps.LoadRun doesn't recognize workspace handle %s" % inputworkspace)
else:
data_file = self._data_file
@@ -255,7 +254,7 @@ def validate_step(func):
kwargs["OutputWorkspace"] = outputworkspace
self.algorithm = alg
- simpleapi.set_properties(alg, *(), **kwargs)
+ mantid.set_properties(alg, *(), **kwargs)
alg.execute()
if "OutputMessage" in propertyOrder:
return alg.getPropertyValue("OutputMessage")
@@ -335,8 +334,8 @@ class Reducer(object):
output_workspaces = []
def __init__(self):
- self.UID = ''.join(
- random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
+ # Generate UUID and trim to 5 chars
+ self.UID = str(uuid.uuid1())[:5]
self.property_manager = "__reduction_parameters_" + self.UID
self._data_files = {}
self._reduction_steps = []
@@ -366,8 +365,8 @@ class Reducer(object):
Removes all workspace flagged as dirty, use when a reduction aborts with errors
"""
for bad_data in self._dirty:
- if bad_data in mtd:
- simpleapi.DeleteWorkspace(Workspace=bad_data)
+ if bad_data in mantid.mtd:
+ mantid.DeleteWorkspace(Workspace=bad_data)
else:
mantid.logger.notice('reducer: Could not access tainted workspace ' + bad_data)
@@ -454,7 +453,7 @@ class Reducer(object):
TODO: this needs to be an ordered list
"""
if data_file is None:
- if workspace in mtd:
+ if workspace in mantid.mtd:
self._data_files[workspace] = None
return
else:
@@ -555,8 +554,7 @@ class ReductionStep(object):
"""
Generate a unique name for an internal workspace
"""
- random_str = ''.join(
- random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
+ random_str = str(uuid.uuid1())[:5]
return "__" + descriptor + "_" + extract_workspace_name(filepath) + "_" + random_str
def execute(self, reducer, inputworkspace=None, outputworkspace=None):
diff --git a/scripts/reduction_workflow/command_interface.py b/scripts/reduction_workflow/command_interface.py
index c75684cba6d4036d55f89bcff1ddd3bcd5471621..6e53918ddba3b4f8b2d5a95dd29e1690e0dc98a3 100644
--- a/scripts/reduction_workflow/command_interface.py
+++ b/scripts/reduction_workflow/command_interface.py
@@ -5,11 +5,9 @@
from reduction_workflow.reducer import Reducer
-
class ReductionSingleton(object):
""" Singleton reduction class """
-
- ## storage for the instance reference
+ # storage for the instance reference
__instance = None
def __init__(self):
@@ -66,7 +64,8 @@ class ReductionSingleton(object):
def get_property_manager(name):
- prop_mng = PropertyManagerDataService.retrieve(name)
+ # prop_mng = mantid.PropertyManagerDataService.retrieve(name)
+ pass
## List of user commands ######################################################
diff --git a/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py b/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
index a00031304af16f927baa590a57cff84c0e74fc85..c858994295cad12b31ac7473d8e4306df0ce6d20 100644
--- a/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
+++ b/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
@@ -8,7 +8,7 @@ List of common user commands for HFIR SANS
import os.path
import mantid
-from reduction_workflow.command_interface import ReductionSingleton, Clear, OutputPath, Reduce1D, Reduce, AppendDataFile, ClearDataFiles
+from reduction_workflow.command_interface import ReductionSingleton, Clear
from reduction_workflow.find_data import find_data
from reduction_workflow.instruments.sans import hfir_instrument
diff --git a/scripts/reduction_workflow/instruments/sans/sns_command_interface.py b/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
index 5adfdacd89f0fe096406df999f7433f1ec0c2a1b..faa594255a283c64210f02d3482638273827bcc5 100644
--- a/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
+++ b/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
@@ -5,35 +5,9 @@
# Import the specific commands that we need - some of these are used in systemtests
from reduction_workflow.command_interface import *
-from hfir_command_interface import DarkCurrent, NoDarkCurrent, NoNormalization
-from hfir_command_interface import SolidAngle, NoSolidAngle
-from hfir_command_interface import DirectBeamCenter, ScatteringBeamCenter
+from hfir_command_interface import SolidAngle
from hfir_command_interface import SetBeamCenter as BaseSetBeamCenter
-from hfir_command_interface import SensitivityCorrection, SetSensitivityBeamCenter
-from hfir_command_interface import SensitivityDirectBeamCenter, SensitivityScatteringBeamCenter
-from hfir_command_interface import NoSensitivityCorrection, DivideByThickness
-
-from hfir_command_interface import IQxQy, NoIQxQy, SaveIq, NoSaveIq, SaveIqAscii
-
-from hfir_command_interface import DirectBeamTransmission, TransmissionDarkCurrent
-from hfir_command_interface import ThetaDependentTransmission
-from hfir_command_interface import SetTransmissionBeamCenter, TransmissionDirectBeamCenter
-from hfir_command_interface import SetTransmission, NoTransmission
-
-from hfir_command_interface import Background, NoBackground, NoBckTransmission
-from hfir_command_interface import SetBckTransmission, BckDirectBeamTransmission
-from hfir_command_interface import SetBckTransmissionBeamCenter, BckThetaDependentTransmission
-from hfir_command_interface import BckTransmissionDirectBeamCenter, BckTransmissionDarkCurrent
-
-from hfir_command_interface import SetSampleDetectorOffset, SetSampleDetectorDistance
-from hfir_command_interface import Mask, MaskRectangle, MaskDetectors, MaskDetectorSide
-from hfir_command_interface import SetAbsoluteScale, SetDirectBeamAbsoluteScale
-from hfir_command_interface import Stitch
-
-#from mantid.api import AlgorithmManager
-#from mantid.kernel import Logger
-#import mantid.simpleapi as simpleapi
from reduction_workflow.find_data import find_data