3DstackDisplay/CreateGIFfromNRRD.py at master · Robbie1977/3DstackDisplay · GitHub

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
import numpy as np
import sys
import nrrd
from images2swf.py import *

colourL=[[0,0,255],[255,0,0],[0,255,0],[255,26,185],[255,211,0],[0,132,246],[0,141,70],[167,97,62],[79,0,106],[0,255,246],[62,123,141],[237,167,255],[211,255,149],[185,79,255],[229,26,88],[132,132,0],[0,255,149],[97,0,44],[246,132,18],[202,255,0],[44,62,0],[0,53,193],[255,202,132],[0,44,97],[158,114,141],[79,185,18],[158,193,255],[149,158,123],[255,123,176],[158,9,0],[255,185,185],[132,97,202],[158,0,114],[132,220,167],[255,0,246],[0,211,255],[255,114,88],[88,62,53],[0,62,53],[220,97,220],[97,114,176],[185,202,44],[18,176,167],[97,18,0],[44,0,44],[88,0,202],[149,193,202],[211,158,35],[132,176,88],[229,237,185],[246,211,255],[185,79,97],[141,9,167],[106,79,0],[0,62,158],[123,62,123],[62,123,97],[167,255,97],[0,149,211],[62,114,0],[176,88,0],[220,0,123],[158,158,255],[79,70,97],[167,255,246],[229,0,44],[114,220,114],[255,237,123],[176,141,70],[97,114,255],[220,70,0],[0,0,114],[9,0,70],[53,237,79],[44,0,0],[167,0,255],[0,246,193],[158,0,44],[0,62,255],[246,158,123],[106,114,53],[255,255,70],[193,176,176],[114,114,114],[193,106,167],[0,88,35],[255,132,141],[176,132,114],[0,70,97],[141,255,18],[176,141,202],[114,79,246],[114,158,0],[211,9,193],[158,0,79],[193,123,255],[141,149,185],[246,167,211],[35,35,9],[255,106,202],[0,141,18],[255,167,88],[229,193,158],[0,18,44],[193,185,88],[0,193,123],[70,44,0],[123,62,88],[158,70,167],[79,88,62],[106,53,185],[114,176,149],[255,176,0],[79,53,132],[185,70,53],[97,167,255],[211,132,149],[123,97,62],[106,0,79],[237,88,255],[149,211,0],[53,167,193],[0,0,158],[123,53,53],[220,255,106],[149,211,79],[132,255,176],[132,53,0],[79,220,229],[70,35,53],[0,44,9],[185,220,193],[88,141,79],[158,114,0],[202,70,132],[0,193,70],[202,9,237],[202,220,255],[0,88,167],[44,167,123],[141,220,255],[35,44,53],[193,255,185],[0,106,158],[0,88,255],[246,88,132],[220,123,70],[202,53,167],[167,202,141],[79,220,193],[97,114,211],[106,35,255],[141,9,202],[220,193,44],[193,185,123],[62,35,88],[123,97,149],[185,123,220],[255,220,211],[237,88,97],[202,185,255],[62,88,88],[114,149,149],[123,255,123],[149,53,106],[202,158,185],[114,62,26],[149,9,141],[246,141,220],[97,176,62],[255,202,97],[211,123,114],[255,237,158],[202,246,255],[88,193,255],[141,97,237],[97,185,114],[141,97,97],[70,70,123],[0,88,211],[88,220,9],[0,26,114],[211,62,44],[149,149,70],[202,123,0],[79,106,141],[149,132,255],[70,35,141],[0,132,132],[246,114,53],[158,220,132],[202,220,106],[176,79,220],[79,9,18],[255,26,123],[123,176,211],[26,0,26],[141,53,246],[88,0,167],[237,141,255]]

if (len(sys.argv) < 2):
    print 'Error: I need at least one image to work with!'
    print 'e.g. python CreateGIFfromNRRD.py firstImage.nrrd [NthImage.nrrd ....]'
else:

    print 'Creating animated GIF...'
    print 'Loading image:', str(sys.argv[1])

    readdata, options = nrrd.read(str(sys.argv[1]))

    im1 = readdata

    Tsize=im1.size

    print 'Calculating final image volume..'

    imN = np.zeros([im1.shape[0]+im1.shape[2],im1.shape[1]+im1.shape[2],im1.shape[1],3],np.uint16)

    print 'Calculating coronal plane area..'
    imC=imN[im1.shape[2]:,0:im1.shape[2],:,:]
    print 'Calculating sagittal plane area..'
    imS=imN[0:im1.shape[2],im1.shape[2]:,:,:]
    print 'Calculating transverse plane area..'
    imT=imN[im1.shape[2]:,im1.shape[2]:,:,:]
    print 'Creating coronal plane slices..'
    imC=np.array(np.reshape(np.repeat(np.transpose(im1,(0,2,1)),3),imC.shape))
    print 'Creating transverse plane slices..'
    imT=np.array(np.repeat(np.reshape(np.repeat(im1[:,:,::-1],3),[imT.shape[0],imT.shape[1],im1.shape[2],imT.shape[3]]),np.int(np.floor(float(im1.shape[1])/float(im1.shape[2]))),2))
    print 'Creating sagittal plane slices..'
    imS=np.array(np.repeat(np.reshape(np.repeat(np.transpose(im1,(2,1,0)),3),[imS.shape[0],imS.shape[1],im1.shape[0],imS.shape[3]]),np.int(np.floor(float(im1.shape[1])/float(im1.shape[0]))),2))

    #multiply intensity with channel colour levels and add to existing signals
    print 'Colouring coronal plane and adding to final image..'
    imN[im1.shape[2]:,0:im1.shape[2],:,:]=np.add(np.uint16(np.multiply((imC/255.0),np.reshape(np.tile(colourL[0],imC.size/3),imC.shape))),imN[im1.shape[2]:,0:im1.shape[2],:,:])
    print 'Colouring sagittal plane and adding to final image..'
    imN[0:im1.shape[2],im1.shape[2]:,:imS.shape[2],:]=np.add(np.uint16(np.multiply((imS/255.0),np.reshape(np.tile(colourL[0],imS.size/3),imS.shape))),imN[0:im1.shape[2],im1.shape[2]:,:imS.shape[2],:])
    print 'Colouring transverse plane and adding to final image..'
    imN[im1.shape[2]:,im1.shape[2]:,:imT.shape[2],:]=np.add(np.uint16(np.multiply((imT/255.0),np.reshape(np.tile(colourL[0],imT.size/3),imT.shape))),imN[im1.shape[2]:,im1.shape[2]:,:imT.shape[2],:])
    print 'Finalising colour merge..'
    imN[imN>255]=np.uint16(255)

    for i in range(2,len(sys.argv)):
        print 'Adding data from ', str(sys.argv[i])
        readdata, options = nrrd.read(str(sys.argv[i]))
        im1 = readdata
        if (Tsize <> im1.size):
            print '\n\nError: Images must be the same size!'
            print 'Skipping: ', str(sys.argv[i])
        else:
            print 'Creating coronal plane slices..'
            imC=np.array(np.reshape(np.repeat(np.transpose(im1,(0,2,1)),3),imC.shape))
            print 'Creating transverse plane slices..'
            imT=np.array(np.repeat(np.reshape(np.repeat(im1[:,:,::-1],3),[imT.shape[0],imT.shape[1],im1.shape[2],imT.shape[3]]),np.int(np.floor(float(im1.shape[1])/float(im1.shape[2]))),2))
            print 'Creating sagittal plane slices..'
            imS=np.array(np.repeat(np.reshape(np.repeat(np.transpose(im1,(2,1,0)),3),[imS.shape[0],imS.shape[1],im1.shape[0],imS.shape[3]]),np.int(np.floor(float(im1.shape[1])/float(im1.shape[0]))),2))

            #multiply intensity with channel colour levels and add to existing signals
            print 'Colouring coronal plane and adding to final image..'
            imN[im1.shape[2]:,0:im1.shape[2],:,:]=np.add(np.uint16(np.multiply((imC/255.0),np.reshape(np.tile(colourL[(i-1)],imC.size/3),imC.shape))),imN[im1.shape[2]:,0:im1.shape[2],:,:])
            print 'Colouring sagittal plane and adding to final image..'
            imN[0:im1.shape[2],im1.shape[2]:,:imS.shape[2],:]=np.add(np.uint16(np.multiply((imS/255.0),np.reshape(np.tile(colourL[(i-1)],imS.size/3),imS.shape))),imN[0:im1.shape[2],im1.shape[2]:,:imS.shape[2],:])
            print 'Colouring transverse plane and adding to final image..'
            imN[im1.shape[2]:,im1.shape[2]:,:imT.shape[2],:]=np.add(np.uint16(np.multiply((imT/255.0),np.reshape(np.tile(colourL[(i-1)],imT.size/3),imT.shape))),imN[im1.shape[2]:,im1.shape[2]:,:imT.shape[2],:])
            print 'Finalising colour merge..'
            imN[imN>255]=np.uint16(255)

    print 'converting to 8-bit..'
    imN=np.uint8(imN)


    #print 'saving NRRD copy as R,G & B images:'
    #print 'Saving red image..'
    #nrrd.write('ResultRedChannel.nrrd',imN[:,:,:,0])
    #print 'Saving green image..'
    #nrrd.write('ResultGreenChannel.nrrd',imN[:,:,:,1])
    #print 'Saving blue image..'
    #nrrd.write('ResultBlueChannel.nrrd',imN[:,:,:,2])


print 'Done.'