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demo.py
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import sys
from brats_toolkit import fusionator, segmentor
seg = segmentor.Segmentor(config='brats_toolkit/config/dockers_demo.json', verbose=True)
seg = segmentor.Segmentor(verbose=True)
seg.runContainer('mic-dkfz', '/test', '/test', 'testseg.nii.gz')
sys.exit(0)
seg2 = segmentor.Segmentor()
fus = fusionator.Fusionator()
t1 = '/Users/christoph/Documents/Uni/HiWi/IBBM/Testdata/BraTS19_CBICA_AQV_1/t1.nii.gz'
t2 = '/Users/christoph/Documents/Uni/HiWi/IBBM/Testdata/BraTS19_CBICA_AQV_1/t2.nii.gz'
t1c = '/Users/christoph/Documents/Uni/HiWi/IBBM/Testdata/BraTS19_CBICA_AQV_1/t1ce.nii.gz'
flair = '/Users/christoph/Documents/Uni/HiWi/IBBM/Testdata/BraTS19_CBICA_AQV_1/flair.nii.gz'
outpath = '/Users/christoph/Documents/Uni/HiWi/IBBM/Testdata/outputForOrc/file2.nii.gz'
print('Test 0 - BRATS MODE')
#fus.dirFuse('/Users/christoph/Desktop/brats_test/', method='brats-simple')
print('Test 1')
seg.segment(t1, t1c, t2, flair, cid='mocker', outputPath=outpath)
print('Test 2')
seg.segment(t1=t1, t1c=t1c, t2=t2, fla=flair,
cid='mocker2', outputPath=outpath)
#seg.segment(t1=t1, t1c=t1c, t2=t2, fla=flair, cid='mocker', outputPath=None)
print('Test 3')
seg.segment(t1=t1, t1c=t1c, t2=t2, fla=flair, cid='simple', outputPath=outpath)
#seg.segment(t1=t1, t1c=t1c, t2=t2, fla=flair, cid='mocker', outputPath='file.nii.gz')
# fus.dirFuse('/Users/christoph/Desktop/brats_test')
# fus.dirFuse('/Users/christoph/Documents/Uni/HiWi/IBBM/BRATUM/Testdata/weborchestra/outputForOrc/')
print('Test 4')
segs = ['/Users/christoph/Desktop/brats_test/BraTS19_Testing_001_mars.nii.gz',
'/Users/christoph/Desktop/brats_test/BraTS19_Testing_001_scan.nii.gz', '/Users/christoph/Desktop/brats_test/BraTS19_Testing_001_zyx.nii.gz']
weights = [1, 2, 1]
fus.fuse(segs, '/Users/christoph/Desktop/brats_test/BraTS19_Testing_fusion_weighted.nii.gz',
method='simple', weights=weights)
fus.fuse(segs, '/Users/christoph/Desktop/brats_test/BraTS19_Testing_fusion_mav.nii.gz', method='mav')
print('Test 5')
# should error out on weight
weights.append(3)
try:
fus.fuse(segs, '/Users/christoph/Desktop/brats_test/BraTS19_Testing_fusion_weighted.nii.gz',
method='simple', weights=weights)
except Exception as e:
print('Error occurred: ' + str(e))
pass
# should error out on file error
print('Test 6')
segs.append('invalid/path/to/nifti/hello.nii.gz')
try:
fus.fuse(segs, '/Users/christoph/Desktop/brats_test/BraTS19_Testing_fusion_weighted.nii.gz',
method='simple', weights=weights)
except Exception as e:
print('Error occurred: ' + str(e))
pass
print('Test 7')
seg.segment(t1=t1, t1c=t1c, t2=t2, fla=flair, cid='mav',
outputPath='/Users/christoph/Documents/Uni/HiWi/IBBM/Testdata/outputForOrc/mav_fusion.nii.gz')
print('Test 8')
#seg.segment(t1=t1, t1c=t1c, t2=t2, fla=flair, cid='mocker2', outputPath=outpath)