-
Notifications
You must be signed in to change notification settings - Fork 0
/
Heidilib.py
650 lines (536 loc) · 21.7 KB
/
Heidilib.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
# -*- coding: utf-8 -*-
import math
import numpy as np
import fractions as fr
from matplotlib import pyplot as plt
import time
from mpl_toolkits.mplot3d import Axes3D
#from decimal import Decimal
HeidiTemperatures={}
Background=[]
#class completePlot(object):#
#def __init__(self,CurrentCrysStruc, measurementFiles, boundaries, options): #boundaries,options should be dictionaries
##self.CurrentCrysStruc=CurrentCrysStruc
#self.measurementFiles=measurementFiles
#self.boundaries=boundaries
#self.option=options
class crystalStructure(object):
"""Class for crystal structures configurations.
"""
def __init__(self,structype=None,a=0.0,b=0.0,c=0.0,alpha=0.0,beta=0.0,gamma=0.0,omat=np.mat(np.identity(3))):
"""initialize a crystal structure configuration
Keyword arguments:
structype -- structure type (default 0.0)
a -- real cell length (default 0.0)
b -- real cell length (default 0.0)
c -- real cell length (default 0.0)
alpha -- real cell angle (default 0.0)
beta -- real cell angle (default 0.0)
gamma -- real cell angle (default 0.0)
omat -- orientation matrix for the defined cell in the form a* b* c*
"""
self.structype=structype
self.a=float(a)
self.b=float(b)
self.c=float(c)
self.alpha=float(alpha) #internal in rad
self.beta=float(beta)
self.gamma=float(gamma)
self.omat=omat#.transpose() #internal is the correct orienting matrix, not a* b* c*
self.omatinv=np.array(np.linalg.inv(self.omat))
if self.a!=0 and self.b!=0 and self.c!=0 and self.alpha!=0 and self.beta!=0 and self.gamma!=0:
self.alphaStar=math.acos((math.cos(self.beta)*math.cos(self.gamma)-math.cos(self.alpha))/(math.sin(self.beta)*math.sin(self.gamma)))
self.betaStar=math.acos((math.cos(self.gamma)*math.cos(self.alpha)-math.cos(self.beta))/(math.sin(self.gamma)*math.sin(self.alpha)))
self.gammaStar=math.acos((math.cos(self.alpha)*math.cos(self.beta)-math.cos(self.gamma))/(math.sin(self.alpha)*math.sin(self.beta)))
if self.structype=='sc':
self.aStar=1/self.a
self.bStar=1/self.b
self.cStar=1/self.c
elif self.structype=='bcc':
self.aStar=2/self.a
self.bStar=2/self.b
self.cStar=2/self.c
elif self.structype=='fcc':
self.aStar=2/self.a
self.bStar=2/self.b
self.cStar=2/self.c
elif self.structype=='hexagonal':
self.aStar=2/(math.sqrt(3)*self.a)#0.103738
self.bStar=2/(math.sqrt(3)*self.b)#0.104386
self.cStar=1/self.c#0.097037
def __eq__(self,other):
"""returns if two crystal structure configurations are equal
Keyword arguments:
other - another crystal structure configuration
"""
return self.structype==other.structype and self.a==other.a and self.b==other.b and self.c==other.c and self.alpha==other.alpha and self.beta==other.beta and self.gamma==other.gamma and self.omat.all()==other.omat.all()
def setValues(self,structype=None,a=0.0,b=0.0,c=0.0,alpha=0.0,beta=0.0,gamma=0.0,omat=np.mat(np.identity(3))):
"""set Values for a crystal structure configuration
Keyword arguments:
structype -- structure type (default 0.0)
a -- real cell length (default 0.0)
b -- real cell length (default 0.0)
c -- real cell length (default 0.0)
alpha -- real cell angle (default 0.0)
beta -- real cell angle (default 0.0)
gamma -- real cell angle (default 0.0)
omat -- orientation matrix for the defined cell in the form a* b* c*
"""
self.structype=structype
self.a=float(a)
self.b=float(b)
self.c=float(c)
self.alpha=float(alpha)#/180.0*math.pi
self.beta=float(beta)#/180.0*math.pi
self.gamma=float(gamma)#/180.0*math.pi
self.omat=omat#.transpose()
#calculate matrixinvers
self.omatinv=np.array(np.linalg.inv(self.omat))
#calculate values for reciprocal cell
self.alphaStar=math.acos((math.cos(self.beta)*math.cos(self.gamma)-math.cos(self.alpha))/(math.sin(self.beta)*math.sin(self.gamma)))
self.betaStar=math.acos((math.cos(self.gamma)*math.cos(self.alpha)-math.cos(self.beta))/(math.sin(self.gamma)*math.sin(self.alpha)))
self.gammaStar=math.acos((math.cos(self.alpha)*math.cos(self.beta)-math.cos(self.gamma))/(math.sin(self.alpha)*math.sin(self.beta)))
#berechne reziproke Zellparameter in kristallographischer Notation
#depending on the structype
if self.structype=='sc':
self.aStar=1/self.a
self.bStar=1/self.b
self.cStar=1/self.c
elif self.structype=='bcc':
self.aStar=2/self.a
self.bStar=2/self.b
self.cStar=2/self.c
elif self.structype=='fcc':
self.aStar=2/self.a
self.bStar=2/self.b
self.cStar=2/self.c
elif self.structype=='hexagonal':
self.aStar=2/(math.sqrt(3)*self.a)#0.103738
self.bStar=2/(math.sqrt(3)*self.b)#0.104386
self.cStar=1/self.c#0.097037
def reset(self):
self.structype=None
self.a=0.0
self.b=0.0
self.c=0.0
self.alpha=0.0
self.beta=0.0
self.gamma=0.0
self.omat=np.mat(np.identity(3)) #internal is the correct orienting matrix, not a* b* c*
self.omatinv=np.array(np.linalg.inv(self.omat))
class HeidiMeasurement(object):
"""A data set from a specific measurement taken at Heidi
"""
def __init__(self,InfoBlock,DatenBlock,Peak,CurrentCrysStruc):
"""initialize a data set
Keyword arguments:
InfoBlock -- Lineblock within gnuplot file, which holds Infodata
DatenBlock -- Lineblock within gnuplot file, which holds the measured data
Peak -- Peak in hkl around which have been measured
CurrentCrysStruc -- the crystal structure of the crystal, which has been measured
"""
self.PeakWinkel=np.array(InfoBlock[0].split('(')[2].split(')')[0].split()).astype(float)
self.theta=self.PeakWinkel[0]
self.omega=self.PeakWinkel[1]
self.chi=self.PeakWinkel[2]
self.phi=self.PeakWinkel[3]
self.Temperatur=float(InfoBlock[0].split('T=')[1].split('K')[0])
self.Peak=Peak
self.time=float(InfoBlock[0].split('t=')[1].split('s')[0])
self.numberOfPoints=int(InfoBlock[0].split('n=')[1].split()[0])
self.domg=float(InfoBlock[0].split('domg=')[1].split()[0])
self.CurrentCrysStruc=CurrentCrysStruc
if InfoBlock[1].find('omega scan')==-1:
print 'Die Messung an %s bei %f K ist kein omega scan' %(self.Peak, self.Temperatur)
#DatenBlock aufteilen
Block=[]
BlockCounter=0
for Zeile in DatenBlock:
#print Zeile
if Zeile.startswith('e'):
if BlockCounter==0:
self.Detector=Block
BlockCounter+=1
elif BlockCounter==1:
self.LRBackground=Block
BlockCounter+=1
elif BlockCounter==2:
self.BackgroundFit=Block
BlockCounter+=1
elif BlockCounter==3:
self.Monitor=Block
BlockCounter+=1
Block=[]
else:
if Zeile.startswith('#'):
Block.append(Zeile)
else:
Block.append(Zeile.split())
#Detectorblock auslesen
self.xomg=[]
self.I=[]
self.Ierr=[]
for Zeile in self.Detector[1:]:
self.xomg.append(float(Zeile[0]))
self.I.append(float(Zeile[1]))
self.Ierr.append(float(Zeile[2]))
self.I=np.array(self.I)
self.Ierr=np.array(self.Ierr)
#LRBackgroundblock auslesen
self.BackgroundPoints=[]
for Zeile in self.LRBackground[1:]:
self.BackgroundPoints.append([float(Zeile[0]),float(Zeile[1])])
#BackgroundFit auslesen
self.BackgroundFitI=[]
for Zeile in self.BackgroundFit[1:]:
self.BackgroundFitI.append(float(Zeile[1]))
self.BackgroundFitI=np.array(self.BackgroundFitI)
#Monitorcounts auslesen
self.MonitorCts=[]
self.MonitorCtserr=[]
for Zeile in self.Monitor[1:]:
self.MonitorCts.append(float(Zeile[1]))
self.MonitorCtserr.append(float(Zeile[2]))
#Berechne aus omg qx,qy,qz
self.q=[]
self.hkl=[]
self.qBetrag=[]
for omgSet in self.xomg:
#print omgSet+self.omega
self.q.append(calcAngles2Koord(self.theta,omgSet+self.omega,self.chi,self.phi,self.CurrentCrysStruc))
#self.hkl.append(calcAngles2Koord(omgSet+self.omega,self.chi,self.phi))
self.qBetrag.append(Betrag(self.q[-1]))
self.qBetrag=np.array(self.qBetrag)
# v Koordinaten des Peaks v #
def get_koord(self):
"""get coordinates of the peak belonging to the measurement
"""
return self._koord
def set_koord(self, Koord):
"""set coordinates of the peak belonging to the measurement
Keyword arguments:
koord -- coordinations in hkl
"""
self._koord=np.array(Koord)
self._qBetrag = BetragInStruk(Koord)
return
def del_koord(self):
"""delete coordinates of the peak belonging to the measurement
"""
del self._koord
return
koord = property(get_koord, set_koord, del_koord, "Koordinaten des Peaks")
# ^ Koordinaten des Peaks ^ #
def Betrag(Vektor):
"""calculate absolute of a vector [Q]
Keyword arguments:
Vektor -- vector defined in Qx,Qy,Qz
"""
return math.sqrt(Vektor[0]**2+Vektor[1]**2+Vektor[2]**2)
def umrechMag2c(Vektor,CurrentCrysStruc):
"""calculate Q from hkl defined by the magnetical structure
Keyword arguments:
Vektor -- vector defined in hkl
CurrentCrysStruc -- the crystal structure of the crystal, which has been measured
"""
#Vektor in magnetischer Zelle definiert in kartesische Koordinaten umrechnen
#Zellparameter
return np.array([CurrentCrysStruc.aStar*Vektor[0]+math.cos(CurrentCrysStruc.gammaStar)*CurrentCrysStruc.bStar*Vektor[1]+CurrentCrysStruc.cStar*Vektor[2]*math.cos(CurrentCrysStruc.alphaStar),CurrentCrysStruc.bStar*math.sin(CurrentCrysStruc.gammaStar)*Vektor[1]+CurrentCrysStruc.cStar*Vektor[2]*math.cos(CurrentCrysStruc.betaStar), CurrentCrysStruc.cStar*Vektor[2]])*2*math.pi
def readHeidiGnuplotFile(filename,CurrentCrysStruc):
"""read a set of measurmeents taken at HEiDi from a gnuplot file and svae them into a dictionary
Keyword arguments:
filename -- filename and path of the gnuplot file to read
CurrentCrysStruc -- the crystal structure of the crystal, which has been measured
"""
file=open(filename,'r')
Zeilen=file.readlines()
HeidiMeasurementDic={}
#Blöcke sind durch leerzeilen getrennt, und infoblock wird vom Datenblock durch '# Detector count rate' getrennt
Zeilen.pop(0)#remove('set terminal postscript color')
Zeilen.pop(0)#remove('set output "' + filename + '"')
InfoBlock=[]
DataBlock=[]
Measurement=[]
for Zeile in Zeilen:
#print len(Zeile)
if Zeile.startswith('set') or Zeile.startswith('plot'):
InfoBlock.append(Zeile)
elif len(Zeile)>1:
DataBlock.append(Zeile)
else:
Peakstring=InfoBlock[0].split('(')[1].split(')')[0]
#print Peakstring
if Peakstring.count('-')==0:
Peak=Peakstring.split()
if len(Peak)==2:
if Peak[0].count('.')>1:
#lpindex=Peakstring.find('.')
rpIndex=Peak[0].rfind('.')
Peakstring=Peak[0][0:rpIndex-2]+ ' ' + Peak[0][rpIndex-2:] + ' ' + Peak[1]
if Peak[1].count('.')>1:
rpIndex=Peak[1].rfind('.')
Peakstring=Peak[0] + ' ' + Peak[1][0:rpIndex-2]+ ' ' + Peak[1][rpIndex-2:]
#print Peakstring
Peak=Peakstring.split()
elif Peakstring.count('-')==1:
index=Peakstring.find('-')
Peakstring=Peakstring[0:index] + ' ' + Peakstring[index:]
#print Peakstring
Peak=Peakstring.split()
if len(Peak)==2:
if Peak[0].count('.')>1:
#lpindex=Peakstring.find('.')
rpIndex=Peak[0].rfind('.')
Peakstring=Peak[0][0:rpIndex-2]+ ' ' + Peak[0][rpIndex-2:] + ' ' + Peak[1]
if Peak[1].count('.')>1:
rpIndex=Peak[1].rfind('.')
Peakstring=Peak[0] + ' ' + Peak[1][0:rpIndex-2]+ ' ' + Peak[1][rpIndex-2:]
#print Peakstring
Peak=Peakstring.split()
elif Peakstring.count('-')==2:
lIndex=Peakstring.find('-')
rIndex=Peakstring.rfind('-')
#print lIndex
#print rIndex
Peakstring=Peakstring[0:lIndex] + ' ' + Peakstring[lIndex:rIndex] + ' ' + Peakstring[rIndex:]
#print Peakstring
Peak=Peakstring.split()
if len(Peak)==2:
if Peak[0].count('.')>1:
#lpindex=Peakstring.find('.')
rpIndex=Peak[0].rfind('.')
Peakstring=Peak[0][0:rpIndex-2]+ ' ' + Peak[0][rpIndex-2:] + ' ' + Peak[1]
if Peak[1].count('.')>1:
rpIndex=Peak[1].rfind('.')
Peakstring=Peak[0] + ' ' + Peak[1][0:rpIndex-2]+ ' ' + Peak[1][rpIndex-2:]
#print Peakstring
Peak=Peakstring.split()
elif Peakstring.count('-')==3:
Peak=Peakstring.split('-')[1:]
Peak=[-float(Peak[0]),-float(Peak[1]),-float(Peak[2])]
Peak=[float(Peak[0]),float(Peak[1]),float(Peak[2])]
#print Peak
Temperatur=InfoBlock[0].split('T= ')[1].split('K')[0]
HeidiMeasurementDic[str(Peak)+ '@' +Temperatur]=HeidiMeasurement(InfoBlock, DataBlock, Peak,CurrentCrysStruc)
InfoBlock=[]
DataBlock=[]
return HeidiMeasurementDic #array mit N Zeilen und 2 Spalten, erster Eintrag InfoBlock, zweiter Eintrag DatenBlock
def unloadHeidiGnuplotFile(HeidiMeasurementDic,unloadDic):
"""remove specific entries from a dictionary
Keyword arguments:
HeidiMeasurementDic -- dictionary conatining measurements form HEiDi
unloadDic -- dictionary containing measurements, which shall be removed from the first one
"""
try:
for key,measurement in unloadDic.iteritems():
del HeidiMeasurementDic[key]
except KeyError:
return False#print 'MeasurementDictionary does not
else:
return True
def calcAngles2Koord(twotheta,omega,chi,phi,CurrentCrysStruc):
"""calculate Q coordinates from the angles of the 4 circle instrument
Keyword arguments:
omega -- omega angle
chi -- chi angle
phi -- phi angle
CurrentCrysStruc -- the crystal structure of the crystal, which has been measured
"""
ca=[0,0,0,0,0]
sa=[0,0,0,0,0]
xyz=[0,0,0,0]
wl=0.87300 #heidi spezifisch
rad=math.pi/180.0
angle=[0,twotheta,omega,chi,phi]
for i in range(1,5):
x=angle[i]*rad
# change 2theta --> theta
if i==1:
x=abs(0.5*x)
sa[i]=math.sin(x)
ca[i]=math.cos(x)
if angle[1]<0:
ca[1]=-ca[1]
x=ca[2]*ca[3];
y=sa[2]*ca[3];
xyz[1]= (ca[1]*(x*ca[4]-sa[2]*sa[4])+sa[1]*(y*ca[4]+ca[2]*sa[4]))#*(-2*math.pi)
xyz[2]=(-ca[1]*(x*sa[4]+sa[2]*ca[4])+sa[1]*(ca[2]*ca[4]-y*sa[4]))#*(-2*math.pi)
xyz[3]= sa[3]*(ca[1]*ca[2]+sa[1]*sa[2])#*2*math.pi
vl=2.0*sa[1]/wl
for i in range(1,4):
xyz[i]*=vl;
oinv=CurrentCrysStruc.omatinv
val=[0,0,0,0]
for i in range(1,4):
val[i]=oinv[i-1][0]*xyz[1]+oinv[i-1][1]*xyz[2]+oinv[i-1][2]*xyz[3]
return umrechMag2c([val[1],val[2],val[3]],CurrentCrysStruc)
def plotteMessung3D(Dictionary,CurrentCrysStruc,hmin=None, hmax=None, kmin=None, kmax=None, lmin=None, lmax=None,Tmin=None,Tmax=None,showNuk=True,showMag=True,showBZ=True,scalePoints=1):#nur Messpunkte unterhalb der angebenen Temperatur plotten
"""plot the measurment data as points within a 3D space
Keyword arguments:
Dictionary -- dictionary conatining measurements form HEiDi, which shall be plotted
CurrentCrysStruc -- the crystal structure of the crystal, which has been measured
hmin -- lower limit for h (default None)
hmax -- upper limit for h (default None)
kmin -- lower limit for k (default None)
kmax -- upper limit for k (default None)
lmin -- lower limit for l (default None)
lmax -- upper limit for l (default None)
Tmin -- lower limit for T (default None)
Tmax -- upper limit for T (default None)
showNuk -- defines if nuclear Peak shall be plotted
showMag -- defines if magnetic Peak shall be plotted
showBZ -- defines if the Brillouinzone shall be plotted
scalePoints -- factor how much the plotted points shall be scaled
"""
import locale
locale.setlocale(locale.LC_NUMERIC, 'C')
#if some of the boundaries were not defined, they are defined as None, then the regarding maximum/minimum shall be selected
if hmin is None:
hmin=1000
for key,Messung in Dictionary.iteritems():
if hmin > Messung.Peak[0]:
hmin=Messung.Peak[0]
if hmax is None:
hmax=-1000
for key,Messung in Dictionary.iteritems():
if hmax < Messung.Peak[0]:
hmax=Messung.Peak[0]
if kmin is None:
kmin=1000
for key,Messung in Dictionary.iteritems():
if kmin > Messung.Peak[1]:
kmin=Messung.Peak[1]
if kmax is None:
kmax=-1000
for key,Messung in Dictionary.iteritems():
if kmax < Messung.Peak[1]:
kmax=Messung.Peak[1]
if lmin is None:
lmin=1000
for key,Messung in Dictionary.iteritems():
if lmin > Messung.Peak[2]:
lmin=Messung.Peak[2]
if lmax is None:
lmax=-1000
for key,Messung in Dictionary.iteritems():
if lmax < Messung.Peak[2]:
lmax=Messung.Peak[2]
if Tmin is None:
Tmin=1000
for key,Messung in Dictionary.iteritems():
if Tmin > Messung.Temperatur:
Tmin=Messung.Temperatur
if Tmax is None:
Tmax=-10000
for key,Messung in Dictionary.iteritems():
if Tmax < Messung.Temperatur:
Tmax=Messung.Temperatur
#print 'h: %i to %i, k: %i to %i, l: %i to %i, T: %f to %f' %(hmin,hmax,kmin,kmax,lmin,lmax,Tmin,Tmax)
fig = plt.figure()
fig.facecolor=1.0
ax = fig.gca(projection='3d')
#ax.set_title('lmin=%s, lmax=%s, showNuk=%s, showMag=%s' %(float('%.1g' % lmin),float('%.1g' % lmax),showNuk,showMag), ha='right')
x=[]
y=[]
z=[]
I=[]
StrukturelleZelleQx=[]
StrukturelleZelleQy=[]
StrukturelleZelleQz=[]
MagReflexe=[]
for l in range(int(math.ceil(lmin)),int(math.floor(lmax+1))):
EckpunktListe=[[0,1,l],[0,2,l],[-1,3,l],[-2,3,l],[-3,4,l],[-3,5,l],[-2,5,l],[-1,4,l],[-1,3,l],[0,2,l],[1,2,l],[1,3,l],[0,4,l],[-1,4,l],[0,4,l],[0,5,l],[1,5,l],[2,4,l],[3,4,l],[4,3,l],[4,2,l],
[3,2,l],[2,3,l],[2,4,l],[2,3,l],[1,3,l],[1,2,l],[2,1,l],[3,1,l],[3,2,l],[4,2,l],[5,1,l],[5,0,l],[6,-1,l],[6,-2,l],[5,-2,l],[6,-2,l],[7,-3,l],[7,-4,l],[6,-4,l],[5,-3,l],[6,-4,l],
[6,-5,l],[5,-5,l],[4,-4,l],[5,-5,l],[5,-6,l],[4,-6,l],[3,-5,l],[3,-4,l],[4,-4,l],[4,-3,l],[5,-3,l],[5,-2,l],[4,-1,l],[4,0,l],[5,0,l],
[4,0,l],[3,1,l],[2,1,l],[2,0,l],[3,-1,l],[4,-1,l],[4,0,l],[4,-1,l],[5,-2,l],[5,-3,l],
[4,-3,l],[4,-4,l],[3,-4,l],[3,-5,l],[2,-5,l],[2,-6,l],[1,-6,l],[0,-5,l],[0,-4,l],[1,-4,l],[2,-5,l],[1,-4,l],[1,-3,l],[2,-3,l],[3,-4,l],[4,-4,l],[4,-3,l],[3,-2,l],[3,-1,l],[3,-2,l],
[2,-2,l],[2,-3,l],[1,-3,l],[0,-2,l],[0,-1,l],[1,-1,l],[2,-2,l],[1,-1,l],[0,-1,l],[-1,0,l],[-1,1,l],[0,1,l],[1,0,l],[1,-1,l],[1,0,l],[2,0,l],[1,0,l],[0,1,l]]
for Eckpunkt in EckpunktListe:
MagReflexe.append(Eckpunkt)
temp=umrechMag2c(Eckpunkt,CurrentCrysStruc)
StrukturelleZelleQx.append(temp[0])
StrukturelleZelleQy.append(temp[1])
StrukturelleZelleQz.append(temp[2])
if showBZ:
ax.plot(StrukturelleZelleQx,StrukturelleZelleQy,StrukturelleZelleQz, label='Bzg der strukturellen Zelle')
#ursprung als rote linie plotten
UrsprungLinie=[[0,0,0],[0,0,lmax]]
UrsprungLinieQx=[]
UrsprungLinieQy=[]
UrsprungLinieQz=[]
for Punkt in UrsprungLinie:
temp=umrechMag2c(Punkt,CurrentCrysStruc)
UrsprungLinieQx.append(temp[0])
UrsprungLinieQy.append(temp[1])
UrsprungLinieQz.append(temp[2])
if showBZ:
ax.plot(UrsprungLinieQx,UrsprungLinieQy,UrsprungLinieQz, label='Normalenvektor der hk0-Ebene', c='r')
NuklearePeaks=[[]]
for key,Messung in Dictionary.iteritems():
if Messung.Peak[0]>=hmin and Messung.Peak[0]<=hmax and Messung.Peak[1]>=kmin and Messung.Peak[1]<=kmax and Messung.Peak[2]>=lmin and Messung.Peak[2]<=lmax and Tmin<Messung.Temperatur and Messung.Temperatur<Tmax:
if Messung.Peak[2]>=lmin and Messung.Peak[2]<=lmax:
if showNuk:
if showMag:
for Punkt,Intens in zip(Messung.q,(Messung.I-Messung.BackgroundFitI)):
x.append(Punkt[0])
y.append(Punkt[1])
z.append(Punkt[2])
I.append(Intens)
elif not showMag:
if MagReflexe.count(Messung.Peak)==0:
for Punkt,Intens in zip(Messung.q,(Messung.I-Messung.BackgroundFitI)):
x.append(Punkt[0])
y.append(Punkt[1])
z.append(Punkt[2])
I.append(Intens)
elif not showNuk:
if showMag:
if MagReflexe.count(Messung.Peak)>0:
for Punkt,Intens in zip(Messung.q,(Messung.I-Messung.BackgroundFitI)):
x.append(Punkt[0])
y.append(Punkt[1])
z.append(Punkt[2])
I.append(Intens)
elif not showMag:
break
if (showNuk or showMag) and len(I)>0:
I=np.array(I)
x=np.array(x)
y=np.array(y)
z=np.array(z)
size=I/I.max()*150*scalePoints/100
color=I/I.max()
idx=np.where(I>0)
ax.scatter(x[idx],y[idx],z[idx], zdir='z', label='zs=0, zdir=z', marker='o', s=size[idx], c=color[idx], edgecolors=None)
#plotte strukturelle Brillouinzone
#dazu Liste der Eckpunkte
ax.legend()
ax.facecolor='white'
ax.set_xlim3d(-0.5, 1.5)
ax.set_ylim3d(-1, 1)
ax.set_zlim3d((lmin-1)*CurrentCrysStruc.cStar*2*math.pi, (lmax+1)*CurrentCrysStruc.cStar*2*math.pi)
plt.show()
return True
else:
return False
def schreibeGnuplotSkript(Dictionary,filename):
"""write a gnuplot script which plots intensity vs. the calculated |Q|
Keyword arguments:
Dictionary -- dictionary conaitning measurements form HEiDi, which shall be plotted
filename -- the file the gnuplotscript shall be written into, and also how the ps -file, from the gnuplot script shall be named like
"""
Datei=open(filename + '.gpl','w')
Datei.write('set terminal postscript color\nset output "%s.ps"\n' %filename)
i=1
for key,Messung in Dictionary.iteritems():
Datei.write('set title " #%i: ( %s ) at ( %s ), t=%fs n=%i domg=%f T=%fK"\n' %(i,Messung.Peak,Messung.PeakWinkel,Messung.time,Messung.numberOfPoints,Messung.domg,Messung.Temperatur))
Datei.write('set xlabel "omega scan, Q [A-1]"\nset ylabel "I [cps]"\n')
Datei.write('set xrange [%f:%f]\n' %(np.min(Messung.qBetrag),np.max(Messung.qBetrag)))
Datei.write('set yrange [%f:%f]\n' %(np.min(Messung.I),np.max(Messung.I)))
Datei.write('plot "-" using 1:($2/ 1.00):($3/ 1.00) with errorbars pt 16 notitle\n')
Datei.write('#Detector count rate - qBetrag - I - Ierr\n')
for Q,I,Ierr in zip(Messung.qBetrag,Messung.I,Messung.Ierr):
Datei.write('\t%f\t%f\t%f\n' %(Q,I,Ierr))
Datei.write('e\n\n')
i+=1
return