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Update CMakeLists.txt #6

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ab7f9f5
Update CMakeLists.txt
johmathe Jan 21, 2019
d81bff3
Update usage_stats.i
johmathe Jan 21, 2019
f774718
Update qs predict for functional api
johmathe Jan 22, 2019
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2 changes: 1 addition & 1 deletion 3rd_party_software/pyca/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -411,7 +411,7 @@ IF(USE_CUDA)

MARK_AS_ADVANCED(CUDA_ARCH_VERSION)
SET(CUDA_ARCH_VERSION
"13"
"30"
CACHE STRING
"Cuda architecture version, ie -arch sm_??")

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1 change: 0 additions & 1 deletion 3rd_party_software/pyca/Code/SWIG/usage_stats.i
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Expand Up @@ -58,7 +58,6 @@ The PyCA team
if msg is not None:
print "Thank you for helping PyCA development"

# save this information locally in _statfile
with open(_statfile, 'w') as f:
f.write(msg)

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35 changes: 15 additions & 20 deletions code/applications/qs_predict.py
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Expand Up @@ -96,7 +96,7 @@ def create_net(args, network_config):
net = torch.nn.DataParallel(net_single, device_ids=device_ids).cuda()
else:
net = net_single

net.train()
return net;
#enddef
Expand All @@ -122,7 +122,7 @@ def write_result(result, output_prefix):


#perform deformation prediction
def predict_image(args):
def predict_image(args, moving_images, target_images, output_prefixes):
if (args.use_CPU_for_shooting):
mType = ca.MEM_HOST
else:
Expand All @@ -144,29 +144,29 @@ def predict_image(args):
correction_net = None;

# start prediction
for i in range(0, len(args.moving_image)):
for i in range(0, len(moving_images)):

common.Mkdir_p(os.path.dirname(args.output_prefix[i]))
common.Mkdir_p(os.path.dirname(output_prefixes[i]))
if (args.affine_align):
# Perform affine registration to both moving and target image to the ICBM152 atlas space.
# Registration is done using Niftireg.
call(["reg_aladin",
"-noSym", "-speeeeed", "-ref", args.atlas ,
"-flo", args.moving_image[i],
"-res", args.output_prefix[i]+"moving_affine.nii",
"-aff", args.output_prefix[i]+'moving_affine_transform.txt'])
"-flo", moving_images[i],
"-res", output_prefixes[i]+"moving_affine.nii",
"-aff", output_prefixes[i]+'moving_affine_transform.txt'])

call(["reg_aladin",
"-noSym", "-speeeeed" ,"-ref", args.atlas ,
"-flo", args.target_image[i],
"-res", args.output_prefix[i]+"target_affine.nii",
"-aff", args.output_prefix[i]+'target_affine_transform.txt'])
"-flo", target_images[i],
"-res", output_prefixes[i]+"target_affine.nii",
"-aff", output_prefixes[i]+'target_affine_transform.txt'])

moving_image = common.LoadITKImage(args.output_prefix[i]+"moving_affine.nii", mType)
target_image = common.LoadITKImage(args.output_prefix[i]+"target_affine.nii", mType)
moving_image = common.LoadITKImage(output_prefixes[i]+"moving_affine.nii", mType)
target_image = common.LoadITKImage(output_prefixes[i]+"target_affine.nii", mType)
else:
moving_image = common.LoadITKImage(args.moving_image[i], mType)
target_image = common.LoadITKImage(args.target_image[i], mType)
moving_image = common.LoadITKImage(moving_images[i], mType)
target_image = common.LoadITKImage(target_images[i], mType)

#preprocessing of the image
moving_image_np = preprocess_image(moving_image, args.histeq);
Expand Down Expand Up @@ -207,11 +207,6 @@ def predict_image(args):

#endif

write_result(registration_result, args.output_prefix[i]);
write_result(registration_result, output_prefixes[i]);
#enddef



if __name__ == '__main__':
check_args(args);
predict_image(args)