-
Notifications
You must be signed in to change notification settings - Fork 0
/
diffusion.py
1411 lines (959 loc) · 31.9 KB
/
diffusion.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
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Author: Eleftherios Garyfallidis
Description: Python library for diffusion MRI
Check testfunctions for examples of usage...
'''
try:
import nifti as ni
volumeloading='ni'
except:
print('Nifti module is not installed. Volumeimages will be used instead')
try:
import volumeimages as vi
volumeloading='vi'
except:
print('Volumeimages is not installed.')
try:
import wx
except:
print('WX module is not installed.')
import os
import sys
import platform
import scipy as sc
import numpy as np
from scipy import linalg
import pickle
try:
import pylab as plt
import matplotlib.axes3d as plt3
except:
print('Pylab module is not installed.')
try:
import wxVTKRenderWindowInteractor as wxvi
except:
print('WX or VTK modules are not installed.')
try:
import vtk
except:
print('VTK module is not installed.')
#try:
# from enthought.tvtk.api import tvtk
# from enthought.tvtk.array_handler import get_vtk_array_type
#except:
# print('Enthought.tvtk module is not installed.')
from ctypes import *
class shared:
project='Tractarian'
opacity=[]
opacityprop=np.array([[ 0.0, 0.0],
[255.0, 0.2]])
color=[]
#colorprop=np.array([[ 0.0, 0.0, 0.0, 0.0],
# [255.0, 1.0, 1.0, 1.0]])
colorprop=np.array([[ 0.0, 0.0, 0.0, 0.0],
[ 64.0, 0.0, 0.0, 1.0],
[128.0, 0.0, 1.0, 0.0],
[192.0, 1.0, 0.0, 0.0],
[255.0, 1.0, 1.0, 1.0]])
im=[]
widget=[]
def __init__(self):
pass
sh=shared()
def loadnifti(fname,info=0):
'''
Returns two arguments
eg. arr,voxsz=loadnifti(filename)
filename should be ending in nii or nii.gz
'''
fname=fname.encode() #change from unicode
if volumeloading=='ni':
img = ni.NiftiImage(fname)
'''
problems with C1 from adam's data 256*256*40*26
'''
arr = img.asarray()
voxsz = img.getVoxDims()
if info==1:
print('Filename: ',fname)
print('Bytes: ',arr.nbytes)
print('Data type: ',arr.dtype.name)
print('Dimensions: ',arr.shape)
return arr,voxsz
elif volumeloading=='vi':
img = vi.load(fname)
arr = np.array(img.get_data())
voxsz = img.get_metadata().get_zooms()
return arr,voxsz
else:
return [],[]
def savenifti(fname,arr,voxsz=(1,1,1)):
if volumeloading=='ni':
nim=ni.NiftiImage(arr)
nim.setVoxDims(voxsz)
nim.save(fname)
elif volumeloading=='vi':
print('Saving with volumeimages not developed yet')
#new_image = vi.Nifti1Image(data, affine)
#vi.save(new_image, 'new_image.nii.gz')
else:
print('Nothing to save')
return
def loadbvals(fname):
bvals = []
for line in open(fname, 'rt'):
bvals =[float(val) for val in line.split()]
bvals=sc.array(bvals)
return bvals
def loadbvecs(fname):
bvecs = []
for line in open(fname, 'rt'):
bvecs.append([float(val) for val in line.split()])
bvecs=sc.array(bvecs)
return bvecs
def filedialog(dlgtype):
'''
dlgtype can be wx.OPEN or wx.SAVE
'''
path = ''; fname = ''; dirname = '';
app = wx.PySimpleApp()
frame = wx.Frame(None, wx.ID_ANY, "Dark", style=wx.STAY_ON_TOP)
#frame.Show(True)
dlg = wx.FileDialog(frame, "Choose a file", fname, "", "*", dlgtype)
if dlg.ShowModal() == wx.ID_OK:
#fname=dlg.GetFilename(); #dirname=dlg.GetDirectory()
path = dlg.GetPath()
dlg.Destroy()
app.MainLoop()
return path
def opendialog():
return filedialog(wx.OPEN)
def savedialog():
return filedialog(wx.SAVE)
def msgdialog(title,msg):
app = wx.PySimpleApp()
frame = wx.Frame(None, wx.ID_ANY, "Dark",style=wx.STAY_ON_TOP)
#frame.Show(True)
dlg= wx.MessageDialog( frame, msg, title, wx.OK)
dlg.ShowModal()
dlg.Destroy()
app.MainLoop()
def systeminfo():
arch=platform.architecture()
release=platform.release()
uname=platform.uname()
plat=sys.platform
pyversion=sys.version.split(' ')[0]
#print(sys.getwindowsversion())
info='This is a '+arch[0]+' '+uname[0]+' os.'
if uname[0]=='Linux':
info2='Exact os version is ' + uname[2]+ '.'
else:
info2='Exact os version is ' + uname[2] +' '+ uname[3]+'.'
info3='The name of this computer is ' + uname[1]+'.'
info4='The version of Python is '+pyversion+'.\n'
print(info)
print(info2)
print(info3)
print(info4)
if uname[0]=='Windows':
try:
from ctypes.wintypes import windll
class MEMORYSTATUS(Structure):
_fields_ = [
('dwLength', DWORD),
('dwMemoryLoad', DWORD),
('dwTotalPhys', DWORD),
('dwAvailPhys', DWORD),
('dwTotalPageFile', DWORD),
('dwAvailPageFile', DWORD),
('dwTotalVirtual', DWORD),
('dwAvailVirtual', DWORD),
]
x = MEMORYSTATUS()
windll.kernel32.GlobalMemoryStatus(byref(x))
print('%d MB physical RAM left.' % (x.dwAvailPhys/1024**2))
print('%d MB physical RAM in total.' % (x.dwTotalPhys/1024**2))
print('%d MB total virtual memory.' % (x.dwTotalVirtual/1024**2))
except:
print('Ctypes.wintypes module is not installed.')
if uname[0]=='Linux':
import re
re_meminfo_parser = re.compile(r'^(?P<key>\S*):\s*(?P<value>\d*)\s*kB')
result = dict()
for line in open('/proc/meminfo'):
match = re_meminfo_parser.match(line)
if not match:
continue # skip lines that don't parse
key, value = match.groups(['key', 'value'])
result[key] = int(value)
print('%d MB total memory.' %(result['MemTotal']/1024))
'''
for cpu usage see /proc/stat
for loadvg see /proc/loadavg
'''
def transp_arr3_vtk(arr):
vol = arr
vol = vol/vol.max()
vol = vol*255
vol = np.round(vol)
vol = np.uint8(vol)
vol = vol.transpose([1,0,2]).copy()
#vol=np.transpose(arr).copy()
#vol.shape = vol.shape[::-1]
return vol
def updateview():
sh.opacity.RemoveAllPoints()
sh.color.RemoveAllPoints()
for i in range(sh.opacityprop.shape[0]):
sh.opacity.AddPoint(sh.opacityprop[i,0],sh.opacityprop[i,1])
for i in range(sh.colorprop.shape[0]):
sh.color.AddRGBPoint(sh.colorprop[i,0],sh.colorprop[i,1],sh.colorprop[i,2],sh.colorprop[i,3])
sh.widget.Render()
def viewvol(arr,voxsz=(1.0,1.0,1.0),maptype=1):
print(arr.dtype)
arr = arr/arr.max()
arr = arr*255
sh.im = vtk.vtkImageData()
#sh.im.SetScalarTypeToFloat()
sh.im.SetScalarTypeToUnsignedChar()
sh.im.SetDimensions(arr.shape[0],arr.shape[1],arr.shape[2])
sh.im.SetOrigin(0,0,0)
sh.im.SetSpacing(voxsz[2],voxsz[0],voxsz[1])
sh.im.AllocateScalars()
print(sh.im.GetNumberOfScalarComponents())
print(arr.shape)
for i in range(arr.shape[0]):
for j in range(arr.shape[1]):
for k in range(arr.shape[2]):
sh.im.SetScalarComponentFromFloat(i,j,k,0,arr[i,j,k])
sh.opacity = vtk.vtkPiecewiseFunction()
for i in range(sh.opacityprop.shape[0]):
sh.opacity.AddPoint(sh.opacityprop[i,0],sh.opacityprop[i,1])
sh.color = vtk.vtkColorTransferFunction()
for i in range(sh.colorprop.shape[0]):
sh.color.AddRGBPoint(sh.colorprop[i,0],sh.colorprop[i,1],sh.colorprop[i,2],sh.colorprop[i,3])
if(maptype==0):
property = vtk.vtkVolumeProperty()
property.SetColor(sh.color)
property.SetScalarOpacity(sh.opacity)
mapper = vtk.vtkVolumeTextureMapper2D()
mapper.SetInput(sh.im)
if (maptype==1):
property = vtk.vtkVolumeProperty()
property.SetColor(sh.color)
property.SetScalarOpacity(sh.opacity)
property.ShadeOn()
property.SetInterpolationTypeToLinear()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
mapper = vtk.vtkVolumeRayCastMapper()
mapper.SetVolumeRayCastFunction(compositeFunction)
mapper.SetInput(sh.im)
ren=vtk.vtkRenderer()
volume = vtk.vtkVolume()
volume.SetMapper(mapper)
volume.SetProperty(property)
ren.AddVolume(volume)
#cone = tvtk.ConeSource(resolution=8)#,height=100, radius=50)
#coneMapper = tvtk.PolyDataMapper(input=cone.get_output())
#coneActor = tvtk.Actor(mapper=coneMapper)
#coneActor.position=sc.array([100.,100.,100.])
#ren.add_actor(coneActor)
#try:
#simplewx(ren,title=sh.project,width=600,height=400)
#except:
simpletk(ren,title=sh.project,width=600,height=400)
return ren
def viewcone():
#'''
cone = vtk.vtkConeSource()
coneMapper = vtk.vtkPolyDataMapper()
coneMapper.SetInput(cone.GetOutput())
coneActor = vtk.vtkActor()
coneActor.SetMapper(coneMapper)
ren = vtk.vtkRenderer()
ren.AddActor(coneActor)
simpletk(ren,title='Cone Demo',width=1024,height=768)
#'''
return
def addpoint(position,radius=0.1,thetares=8,phires=8,color=(0,0,1),opacity=1):
sphere = vtk.vtkSphereSource()
sphere.SetRadius(radius)
sphere.SetThetaResolution(thetares)
sphere.SetPhiResolution(phires)
spherem = vtk.vtkPolyDataMapper()
spherem.SetInput(sphere.GetOutput())
spherea = vtk.vtkActor()
spherea.SetMapper(spherem)
spherea.SetPosition(position)
spherea.GetProperty().SetColor(color)
spherea.GetProperty().SetOpacity(opacity)
return spherea
def addline(pos1,pos2,color=(1,0,0),res=1):
line=vtk.vtkLineSource()
line.SetResolution(res)
line.SetPoint1(pos1)
line.SetPoint2(pos2)
linem = vtk.vtkPolyDataMapper()
linem.SetInput(line.GetOutput())
linea = vtk.vtkActor()
linea.SetMapper(linem)
linea.GetProperty().SetColor(color)
return linea
def addarrow(pos=(0,0,0),color=(1,0,0),opacity=1):
arrow = vtk.vtkArrowSource()
arrowm = vtk.vtkPolyDataMapper()
arrowm.SetInput(arrow.GetOutput())
arrowa= vtk.vtkActor()
arrowa.SetMapper(arrowm)
arrowa.GetProperty().SetColor(color)
arrowa.GetProperty().SetOpacity(opacity)
return arrowa
def addaxes():
arrowx=addarrow(color=(1,0,0))
arrowy=addarrow(color=(0,1,0))
arrowz=addarrow(color=(0,0,1))
arrowy.RotateZ(90)
arrowz.RotateY(-90)
ass=vtk.vtkPropAssembly()
ass.AddPart(arrowx)
ass.AddPart(arrowy)
ass.AddPart(arrowz)
return ass
def addlabel(ren,text='Origin',pos=(0,0,0),scale=(0.1,0.1,0.1)):
atext=vtk.vtkVectorText()
atext.SetText(text)
textm=vtk.vtkPolyDataMapper()
textm.SetInput(atext.GetOutput())
texta=vtk.vtkFollower()
texta.SetMapper(textm)
texta.SetScale(scale)
texta.SetPosition(pos)
ren.AddActor(texta)
texta.SetCamera(ren.GetActiveCamera())
return texta
def addaxeswithlabels(length=(1,1,1),labelx="x",labely="y",labelz="z"):
axes=vtk.vtkAxesActor()
#axes.SetShaftTypeToCylinder()
axes.SetXAxisLabelText(labelx)
axes.SetYAxisLabelText(labely)
axes.SetZAxisLabelText(labelz)
axes.SetTotalLength(length)
tprop = vtk.vtkTextProperty()
tprop.ItalicOn()
tprop.ShadowOn()
tprop.SetFontFamilyToTimes()
axes.GetXAxisCaptionActor2D().SetCaptionTextProperty(tprop)
tprop2 = vtk.vtkTextProperty()
tprop2.ShallowCopy(tprop)
axes.GetYAxisCaptionActor2D().SetCaptionTextProperty(tprop2)
tprop3 = vtk.vtkTextProperty()
tprop3.ShallowCopy(tprop)
axes.GetZAxisCaptionActor2D().SetCaptionTextProperty(tprop3)
return axes
def viewscatter(listofpoints):
ren=vtk.vtkRenderer()
#ren.AddActor(addaxeswithlabels(length=(10,10,10)))
ren.AddActor(addaxes())
ren.AddActor(addline(pos1=(-10,0,0),pos2=(10,0,0),color=(1,0,0)))
ren.AddActor(addline(pos1=(0,-10,0),pos2=(0,10,0),color=(0,1,0)))
ren.AddActor(addline(pos1=(0,0,-10),pos2=(0,0,10),color=(0,0,1)))
for var in listofpoints:
ren.AddActor(addpoint(position=var))
#ren.AddActor(addlabel())
addlabel(ren)
simpletk(ren,title='Scatter Plot',width=1024,height=768)
def simpletk(ren,title='Tractarian',width=600,height=400):
print('Using tk')
picker = vtk.vtkCellPicker()
def annotatePick(object, event):
if picker.GetCellId() < 0:
print('No object')
print(np.round(picker.GetSelectionPoint(), decimals=2))
else:
print('Object Found')
print(np.round(picker.GetSelectionPoint(), decimals=2))
print(np.round(picker.GetPickPosition(), decimals=2))
print(np.round(picker.GetActors().GetLastActor().GetPosition(), decimals=2))
picker.AddObserver("EndPickEvent", annotatePick)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.SetPicker(picker)
renWin.SetSize(width,height)
renWin.Render()
renWin.SetWindowName(title)
def CheckAbort(obj, event):
if obj.GetEventPending() != 0:
obj.SetAbortRender(1)
renWin.AddObserver("AbortCheckEvent", CheckAbort)
sh.widget=renWin
iren.Initialize()
picker.Pick(0, 0, 0, ren)
renWin.Render()
iren.Start()
return
def simplewx(ren,title='Tractarian',width=600,height=400):
'''
Create a simple wx window and render vtk inside
'''
print('Using wx')
app = wx.PySimpleApp()
frame = wx.Frame(None, -1, title, size=(width,height))
sh.widget = wxvi.wxVTKRenderWindowInteractor(frame, -1)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(sh.widget, 1, wx.EXPAND)
frame.SetSizer(sizer)
frame.Layout()
sh.widget.Enable(1)
sh.widget.AddObserver("ExitEvent", lambda o,e,f=frame: f.Close())
sh.widget.GetRenderWindow().AddRenderer(ren)
frame.Show()
app.MainLoop()
return
def threshold(arr, lower=0, upper=100):
'''
Threshold array arr using an upper and lower threshold in % (percentage)
e.g threshold(arr, 20, 70)
'''
if lower<0:
print('lower threshold cannot be smaller than 0')
return
if upper>100:
print('upper threshold cannot be higher than 100')
return
if upper<lower:
print('upper cannot be smaller than lower')
return
min=arr.min()
max=arr.max()
y=lower
x=((max-min)/100.0)*y+min
print('lower:',x)
arr[arr<x]=0
y=upper
x=((max-min)/100.0)*y+min
print('upper:',x)
arr[arr>x]=0
return
def slider(title='Slider',size=(478,94)):
class MyFrame(wx.Frame):
def __init__(self, *args, **kwds):
kwds["style"] = wx.DEFAULT_FRAME_STYLE
wx.Frame.__init__(self, *args, **kwds)
self.slider_1 = wx.Slider(self, -1, 0, 0, 10, style=wx.SL_HORIZONTAL|wx.SL_LABELS)
self.__set_properties()
self.__do_layout()
self.Bind(wx.EVT_COMMAND_SCROLL, self.OnScroll, self.slider_1)
def __set_properties(self):
self.SetTitle(title)
self.SetSize(size)
self.SetBackgroundColour(wx.Colour(0, 0, 0))
self.slider_1.SetBackgroundColour(wx.Colour(0, 0, 0))
self.slider_1.SetForegroundColour(wx.Colour(255, 255, 255))
self.slider_1.SetFont(wx.Font(8, wx.DEFAULT, wx.NORMAL, wx.NORMAL, 0, ""))
def __do_layout(self):
sizer_1 = wx.BoxSizer(wx.VERTICAL)
sizer_1.Add(self.slider_1, 0, wx.EXPAND, 0)
self.SetSizer(sizer_1)
self.Layout()
def OnScroll(self, event):
obj=self.slider_1.GetValue()
event.Skip()
app = wx.PySimpleApp(0)
wx.InitAllImageHandlers()
frame_1 = MyFrame(None, -1, "")
app.SetTopWindow(frame_1)
frame_1.Show()
app.MainLoop()
return
def plotarr3(arr,point=(0,0,0)):
#if arr.ndim != 3:
# print('arr can only be 3d')
# return
print(point[0])
print(point[1])
print(point[2])
axial = arr[point[0]]
coronal=arr[:,point[1]]
saggital=arr[:,:,point[2]]
plotarr2(axial,'Axial')
plotarr2(coronal,'Coronal')
plotarr2(saggital,'Saggital')
'''
doplt = partial(plt.imshow, origin='lower', cmap=plt.jet())
doplt(arr[42])
plt.title('Axial slice')
plt.show()
plt.figure()
doplt(arr[:,42])
plt.title('Coronal slice')
plt.show()
plt.figure()
doplt(arr[:,:,42])
plt.title('Sagittal slice')
plt.show()
'''
return
def plotarr2(mat,title):
#if arr.ndim != 2:
# print('arr can only be 2d')
# return
plt.figure()
plt.imshow(mat,origin='lower',cmap=plt.jet())
plt.title(title)
plt.show()
def viewgl(list):
return
def main():
print('In main')
return
def testvol():
fname=opendialog()
#fname='FAsimple.nii.gz'
print(fname)
arr,voxsz=loadnifti(fname)
print(arr.shape)
if arr.ndim ==4:
viewvol(arr[0],voxsz)
elif arr.ndim==3:
viewvol(arr,voxsz)
else:
print('Please use only 3d or 4d volumes')
#df.sh.opacity.add_point(255,0.2)
#df.sh.widget.Render()
def testvolsl():
fname=opendialog()
arr,voxsz=loadnifti(fname)
sz=arr.shape
ker=np.zeros(sz)
msk=np.ones((sz[1],sz[2]))
ker[sz[0]/2]=msk
arr=arr*ker
viewvol(arr,voxsz)
def axialfilter(arr,no):
sz=arr.shape
ker=np.zeros(sz)
msk=np.ones((sz[1],sz[2]))
ker[no]=msk
arr=arr*ker
return arr,ker
def coronalfilter(arr,no):
sz=arr.shape
ker=np.zeros(sz)
msk=np.ones((sz[0],sz[2]))
ker[:,no]=msk
arr=arr*ker
return arr,ker
def saggitalfilter(arr,no):
sz=arr.shape
ker=np.zeros(sz)
msk=np.ones((sz[0],sz[1]))
ker[:,:,no]=msk
arr=arr*ker
return arr,ker
def slicerfilter(arr,point=(0,0,0)):
if arr.ndim != 3:
print('arr needs to be 3d')
arr1,ker1=axialfilter(arr,point[0])
arr2,ker2=coronalfilter(arr,point[1])
arr3,ker3=saggitalfilter(arr,point[2])
ker12=np.logical_or(ker1,ker2)
ker=np.logical_or(ker12,ker3)
arr=arr*ker
return arr
def testnifti():
'''
Create some simulated data in a numpy array and save them as a niftiimage.
Then load them again from the disk in memory and visualize them with viewvol.
'''
dims=(60,60,60)
x, y, z = sc.ogrid[-5:5:dims[0]*1j,-5:5:dims[1]*1j,-5:5:dims[2]*1j]
x = x.astype('f')
y = y.astype('f')
z = z.astype('f')
scalars = (sc.sin(x*y*z)/(x*y*z))
fname='test.nii.gz'
savenifti(fname,scalars,voxsz=(1,1,1))
arr,voxsz=loadnifti(fname)
viewvol(arr,voxsz)
def testplotarr3():
fname=opendialog()
arr,voxsz=loadnifti(fname)
print(arr.ndim)
print(arr.shape)
plotarr3(arr,point=(42,42,42))
def tensorfitsimple(arr,bvals,bvecs,mskthr=100.0,averaging=1):
'''
Optimized version of tensorfit
Calculate tensors from a 4d numpy array and return an FA image.
bvals and bvecs must be provided as well.
FA calculated from Mori et.al, Neuron 2006
In WindowsXP the memory used can be ~1GB where it is a problem
with the amount of diffusion data.
'''
if arr.ndim!=4:
print('Please provide a 4d numpy array as arr here')
return
B=bvals.astype('float32')
G=bvecs.astype('float32')
imshape=arr.shape
volshape=(imshape[1],imshape[2],imshape[3])
volnos=arr.shape[0]
arr=arr.astype('float32')
vollen=volshape[0]*volshape[1]*volshape[2]
if averaging==1:
arr[0:volnos/2]=0.5*(arr[0:volnos/2]+arr[volnos/2:volnos])
S=arr[0:volnos/2].copy()
del arr,bvals,bvecs
A=sc.zeros((volnos/2-1,6))
FA=sc.zeros(volshape,dtype='float32')
msk=sc.zeros(volshape,dtype='float32')
S0=S[0]
msk[S0<mskthr]=1
S[S<1.0]=1.0
S=sc.log(S)
S=S[0]-S[:]
S=S[1:]
#try simple tensor fit
for i in sc.arange(volnos/2-1):
b=B[i+1]
g=G[:,i+1]
g1=g[0]; g2=g[1]; g3=g[2]
A[i,0]=g1*g1
A[i,1]=g2*g2
A[i,2]=g3*g3
A[i,3]=2*g1*g2
A[i,4]=2*g1*g3
A[i,5]=2*g2*g3
S[i]=S[i]/b
S=S.reshape(volnos/2-1,vollen)
FA=FA.reshape(vollen)
msk=msk.reshape(vollen)
d,resids,rank,sing=sc.linalg.lstsq(A,S)
cnt=0
#D=sc.array([[d11,d12,d13],[d12,d22,d23],[d13,d23,d33]])
D=sc.zeros((3,3))
for i in sc.arange(vollen):
if msk[i]== 1:
FA[i]=0
else:
#d11=d[0,i]; d22=d[1,i]; d33=d[2,i]; d12=d[3,i]; d13=d[4,i]; d23=d[5,i];
D[0,0]=d[0,i];
D[1,1]=d[1,i];
D[2,2]=d[2,i];
D[0,1]=d[3,i];
D[0,2]=d[4,i];
D[1,2]=d[5,i];
D[1,0]=D[0,1]
D[2,0]=D[0,2]
D[2,1]=D[1,2]
evals,evecs=sc.linalg.eig(D)
l1=evals[0];l2=evals[1];l3=evals[2]
if l1<0 or l2<0 or l3<0:
cnt+=1
FA[i]=sc.sqrt( ( (l1-l2)**2 + (l2-l3)**2 + (l3-l1)**2 )/( 2*(l1**2+l2**2+l3**2) ) )
print('Not positive definite ',cnt, ' times.')
FA=FA.reshape(volshape[0],volshape[1],volshape[2])
del S,A,msk
return FA
def residuals_example(p, y, x):
A,k,theta = p
err = y-A*sc.sin(2*sc.pi*k*x+theta)
return err
def testnonlinearlsqexample():
x = sc.arange(0,6e-2,6e-2/30)
A,k,theta = 10, 1.0/3e-2, sc.pi/6
y_true = A*sc.sin(2*sc.pi*k*x+theta)
y_meas = y_true + 2*sc.randn(len(x))
p0 = [8, 1/2.3e-2, sc.pi/3]
print(p0)
from scipy.optimize import leastsq
plsq = leastsq(residuals_example, p0, args=(y_meas, x),full_output=1)
print(plsq)
#from scipy.optimize import anneal
#xann = anneal(residuals_example, p0, args=(y_meas,x),schedule='cauchy')
#print(xann[0])
'''
def residuals_rosenbrock(x1,x2):
return 100*(x2-x1**2)**2+(1-x1)**2
def testoptimizationalgs():
x0=[1,1]
from scipy.optimize import leastsq
x=leastsq(residuals_rosenbrock,