def recon_with_scatter(json_path, outdir):
tf.enable_eager_execution()
if outdir is None:
outdir = os.path.dirname(os.path.abspath(json_path))
else:
outdir = os.path.abspath(outdir)
mlem_full_without_data = nef.io.json_load(nef.functions.MlemFull,
json_path)
mlem_obj = nef.io.load_all_data(mlem_full_without_data)
img = nef.load(nef.Image, outdir + '/recon_image.hdf5')
if mlem_obj.scatter_corr is not None:
listmode = mlem_obj.scatter_corr(img, mlem_obj.atten_corr.u_map,
mlem_obj.scanner, outdir)
listmode = nef.ListmodeCompress(scanner)(listmode)
mlem_full = nef.MlemFull(mlem_obj.n_iter, mlem_obj.image_config,
mlem_obj.scanner, listmode)
img = mlem_full()
nef.save(img, outdir + '/recon_image_scatter.hdf5')
nef.save(mlem_full_without_data, outdir + '/mlem_full_scatter.hdf5')
nef.doc_gen(mlem_full_without_data, img, outdir,
outdir + '/recon_doc_scatter.md')
pypandoc.convert_file(outdir + '/recon_doc_scatter.md',
'pdf',
outputfile=outdir + '/recon_doc_scatter.md' +
'.pdf')
return img
def recon_full(json_path, outdir):
tf.enable_eager_execution()
if outdir is None:
outdir = os.path.dirname(os.path.abspath(json_path))
else:
outdir = os.path.abspath(outdir)
if not os.path.isdir(outdir):
os.mkdir(outdir, mode=0o777)
mlem_full_without_data = nef.io.json_load(nef.functions.MlemFull,
json_path)
mlem_obj = nef.io.load_all_data(mlem_full_without_data)
img = mlem_obj()
from srfnef.corrections.scattering.scatter import scatter_preprocess
if mlem_obj.scatter_corr is not None:
scatter_preprocess(mlem_obj.scanner, mlem_obj.listmode, img,
mlem_obj.atten_corr.u_map, outdir)
nef.save(img, outdir + '/recon_image.hdf5')
# nef.save(mlem_full_without_data, outdir + '/mlem_full.hdf5')
nef.doc_gen(mlem_full_without_data, img, outdir, outdir + '/recon_doc.md')
pypandoc.convert_file(outdir + '/recon_doc.md',
'pdf',
outputfile=outdir + '/recon_doc.md' + '.pdf')
return img
def test_full(json_path, outdir, system):
tf.compat.v1.enable_eager_execution()
if outdir is None:
outdir = os.path.dirname(os.path.abspath(json_path))
else:
outdir = os.path.abspath(outdir)
if not os.path.isdir(outdir):
os.mkdir(outdir, mode=0o777)
# if system == 'mct':
mlem_full_without_data = nef.io.json_load(nef.functions.MlemFull,
json_path)
if system == '8panel':
with open('/mnt/users/weijie/srfnef/mlem_full.json', 'r') as fin:
dct = json.load(fin)
scanner = nef.PetCylindricalScanner.from_dict(dct['scanner'])
mlem_full_without_data = mlem_full_without_data.update(scanner=scanner)
mlem_obj = nef.io.load_all_data(mlem_full_without_data)
opt_atten = [None] if mlem_obj.atten_corr is None else [
None, mlem_obj.atten_corr
]
opt_psf = [None
] if mlem_obj.psf_corr is None else [None, mlem_obj.psf_corr]
for atten in opt_atten:
for psf in opt_psf:
out_append = ''
if atten is not None:
out_append += '_atten'
if psf is not None:
out_append += '_psf'
print('*************************************************')
print(out_append)
mlem_ = mlem_obj.update(atten_corr=atten,
psf_corr=psf,
scatter_corr=None)
img = mlem_()
from srfnef.corrections.scattering.scatter import scatter_preprocess
scatter_preprocess(mlem_obj.scanner,
mlem_obj.listmode,
img,
mlem_obj.atten_corr.u_map,
outdir,
out_append=out_append)
nef.save(img, outdir + f'/recon_image{out_append}.hdf5')
# with open(json_path, 'r') as fin:
# if 'mask' in json.load(fin):
# mask_path = json.load(fin)['mask']
# else:
# mask_path = None
nef.doc_gen(mlem_full_without_data, img, outdir,
outdir + f'/recon_doc{out_append}.md')
pypandoc.convert_file(outdir + f'/recon_doc{out_append}.md',
'pdf',
outputfile=outdir +
f'/recon_doc{out_append}.md' + '.pdf')
return img
def test_with_scatter(json_path, outdir, system):
tf.enable_eager_execution()
if outdir is None:
outdir = os.path.dirname(os.path.abspath(json_path))
else:
outdir = os.path.abspath(outdir)
if not os.path.isdir(outdir):
os.mkdir(outdir, mode=0o777)
mlem_full_without_data = nef.io.json_load(nef.functions.MlemFull,
json_path)
if system == '8panel':
with open('/mnt/users/weijie/srfnef/mlem_full.json', 'r') as fin:
dct = json.load(fin)
scanner = nef.PetCylindricalScanner.from_dict(dct['scanner'])
mlem_full_without_data = mlem_full_without_data.update(scanner=scanner)
mlem_obj = nef.io.load_all_data(mlem_full_without_data)
opt_atten = [None] if mlem_obj.atten_corr is None else [
None, mlem_obj.atten_corr
]
opt_psf = [None
] if mlem_obj.psf_corr is None else [None, mlem_obj.psf_corr]
for atten in opt_atten:
for psf in opt_psf:
out_append = ''
if atten is not None:
out_append += '_atten'
if psf is not None:
out_append += '_psf'
print('*************************************************')
print("scattering")
img = nef.load(nef.Image,
outdir + f'/recon_image{out_append}.hdf5')
listmode = mlem_obj.scatter_corr(img, mlem_obj.atten_corr.u_map,
mlem_obj.scanner, outdir,
out_append)
mlem_ = nef.MlemFull(mlem_obj.n_iter, mlem_obj.image_config,
mlem_obj.scanner, listmode)
img = mlem_()
out_append += '_scatter'
print(out_append)
nef.save(img, outdir + f'/recon_image{out_append}.hdf5')
nef.doc_gen(mlem_full_without_data, img, outdir,
outdir + f'/recon_doc{out_append}.md')
pypandoc.convert_file(outdir + f'/recon_doc{out_append}.md',
'pdf',
outputfile=outdir +
f'/recon_doc{out_append}.md' + '.pdf')
return img
def extract_listmode(path, nsub, outpath, system):
path = path.replace('sub.0', 'sub.?')
if system == 'mct':
listmode = listmode_from_gate_out(path, nef.scanner_mct, int(nsub))
else:
raise NotImplementedError
if not outpath.endswith('.hdf5'):
outdir = outpath
if not os.path.isdir(outdir):
os.mkdir(outdir, mode = 0o777)
outpath = outdir + '/listmode_trans.hdf5'
else:
pass
nef.save(listmode, outpath)
print(outpath)
def recon_full(json_path, outdir):
if outdir is None:
outdir = os.path.dirname(os.path.abspath(json_path))
else:
outdir = os.path.abspath(outdir)
if not os.path.isdir(outdir):
os.mkdir(outdir, mode=0o777)
mlem_full_without_data = nef.io.json_load(
nef.functions.MlemFullCylindrical, json_path)
mlem_obj = nef.io.load_all_data(mlem_full_without_data)
img = mlem_obj()
nef.save(img, outdir + '/recon_image.hdf5')
nef.save(mlem_full_without_data, outdir + '/mlem_full.hdf5')
nef.doc_gen(mlem_full_without_data, img, outdir, outdir + '/recon_doc.md')
pypandoc.convert_file(outdir + '/recon_doc.md',
'pdf',
outputfile=outdir + '/recon_doc.md' + '.pdf')
return img
def recon_simple(listmode_path, outdir, system, n_iter):
listmode = nef.load(nef.Listmode, listmode_path)
if system == 'mct':
image_config = nef.image_config_mct
scanner = nef.scanner_mct
else:
raise NotImplementedError
mlem_full = nef.MlemFull(n_iter, image_config, scanner, listmode)
mlem_full_without_data = mlem_full.update(listmode = listmode_path)
img = mlem_full()
if outdir == '.':
pass
elif not os.path.isdir(outdir):
os.mkdir(outdir, mode = 0o777)
nef.save(img, outdir + '/recon_image.hdf5')
nef.save(mlem_full, outdir + '/mlem_full.hdf5')
doc_path = nef.doc_gen(mlem_full_without_data, img, outdir, outdir + '/recon_doc.md')
print('generating doc at', doc_path)
pypandoc.convert_file(outdir + '/recon_doc.md', 'pdf',
outputfile = outdir + '/recon_doc.md' + '.pdf')
return img