def test_div(self):
with self.subTest(0):
p = Path('/tmp')
p = p / 'sub'
self.assertEqual(p.route, '/tmp/sub')
with self.subTest(1):
p = Path('/tmp')
p = p / 'sub/'
self.assertEqual(p.route, '/tmp/sub')
def lm2bin(config, target):
path_file = config['input']['listmode']['path_file']
data = load_h5(path_file)
coo_data = np.hstack((data['fst'], data['snd']))
bin_data = np.hstack(
(coo_data, data['weight'].reshape(data['weight'].size, 1)))
out = bin_data.astype(np.float32)
out.tofile((Path(target) + 'input.txt').abs)
f = open((Path(target) + 'input.txt.hdr').abs, 'w')
f.write(str(out.shape[0]))
def setUp(self):
dpath = tempfile.mkdtemp()
dpath1 = tempfile.mkdtemp()
pdr = Path(dpath)
pf1 = Directory(pdr / 'sub1')
mkdir(pf1)
pf2 = Directory(pdr / 'sub2')
mkdir(pf2)
pd6 = pdr / 'sub6'
mkdir(Directory(pd6))
pd7 = Directory(pd6 / 'sub7')
mkdir(pd7)
self.root = dpath
self.root1 = Path(dpath1)
def save_script(path, data):
path = Path(path)
if path.suffix == ' ':
path = path + 'hs'
target = path.abs
with open(target, 'w') as fin:
fin.write(data)
def save_script(path, data, suffix):
path = Path(path)
if path.suffix == '':
path = path + suffix
target = path.abs
with open(target, 'w') as fout:
fout.write(data)
def save_osem_result(save_path, dataset_prefix, source, nb_iterations,
nb_subsets):
with h5py.File(save_path.abs) as fout:
for i in range(0, nb_iterations):
for j in range(0, nb_subsets):
label = dataset_prefix + 'output_' + str(i + 1) + '_' + str(j +
1)
source_path = Path(source) + str(i + 1) + '_' + str(j +
1) + '.v'
fout[label] = np.fromfile(source_path.abs, dtype='float32')
def generate_recon_script(config, target, source):
with open(config, 'r') as fin:
c = json.load(fin)
if source is None:
source = '.'
recon_spec = generatereconspec(c, source)
recon_script = render(ReconstructionSpecScript(recon_spec))
path_script = Path(target).abs + '/OSMAPOSL.par'
# if path_script.suffix == ' ':
# path_script = path_script+'.par'
save_script(path_script, recon_script)
def test_parts(self):
with self.subTest(0):
p = Path('/tmp/base')
self.assertEqual(p.parts(), ('/', 'tmp', 'base'))
with self.subTest(1):
p = Path('a/b')
self.assertEqual(p.parts(), ('a', 'b'))
def save_result(config, source):
part_config = config['algorithm']['recon']
nb_subsets, nb_subiterations = get_iter_info(part_config)
algorithm = get_algorithm(part_config)
save_path = Path(config['output']['image']['path_file'])
dataset_prefix = config['output']['image']['path_dataset_prefix']
if algorithm == ('FBP2D' or 'FBP3DRP'):
save_fbp_result(save_path, dataset_prefix, source)
elif algorithm == 'MLEM':
save_mlem_result(save_path, dataset_prefix, source, nb_subiterations)
else:
save_osem_result(save_path, dataset_prefix, source, nb_subiterations,
nb_subsets)
def generatereconspec(config, path_header):
path_header = Path(path_header + '/sinogram.hs')
part_config = config['algorithm']['recon']
if ("osem" in part_config):
nb_subsets = part_config['osem']['nb_subsets']
nb_subiterations = part_config['osem']['nb_iterations']
else:
nb_subsets = 1
nb_subiterations = part_config['mlem']['nb_iterations']
return ReconstructionSpec(path_header.abs,
config['output']['image']['grid'][0], nb_subsets,
nb_subiterations)
def generate_data_and_header(config, target):
with open(config, 'r') as fin:
c = json.load(fin)
scanner = get_scanner(c['scanner']['petscanner'])
path_data = Path(target)
gen_sino_script(c['scanner']['petscanner'], (path_data.abs + 'sinogram'))
path_file = c['input']['listmode']['path_file']
data = load_h5(path_file)
lor = List(
LoR(PositionEvent(data['fst'][i, ]),
PositionEvent(data['snd'][i, ]),
weight=data['weight'][i]) for i in range(0, data['weight'].size))
lm2sino(scanner, lor, (path_data.abs + '/sinogram.s'))
def setUp(self):
dpath = tempfile.mkdtemp()
dpath1 = tempfile.mkdtemp()
pdr = Path(dpath)
pf1 = File(pdr / 'tmp.txt')
touch(pf1)
pf2 = File(pdr / 'tmp2.txt')
touch(pf2)
pf3 = File(pdr / 'tmp4.txt')
touch(pf3)
with open(str(pf3.path), 'w') as fout:
print('test3', file=fout)
self.root = dpath
self.root1 = dpath1
def test_copy_file(self):
file1 = File(self.root + '/tmp2.txt')
cp(file1, Path(self.root1 + '/tmp2.txt'))
file2 = File(self.root1 + '/tmp2.txt')
assert file2.exists and file1.exists
def neg1():
path2 = Path(self.root + '/tmpx.txt')
assert not File.is_file(path2)
def neg2():
path3 = Path(self.root + '/sub1')
assert not File.is_file(path3)
def neg():
file1 = File((Path(self.root) / 'tmpx.txt').abs)
assert not (file1.exists)
def pos():
path1 = Path(self.root + '/tmp.txt')
assert File.is_file(path1)
def test_fatherpath(self,input,output):
assert Path(input).father_path().route ==output
def pos():
file1 = File((Path(self.root) / 'tmp.txt').abs)
assert (file1.exists)
def test_absolute(self,input,output):
assert Path(input).absolute().route == output
def test_dot(self):
self.assertEqual(Path('.').route, '')
def test_eq(self,xi,xo):
assert Path(xi) == Path(xo)
def test_relative(self,input,output):
assert Path(input).relative == output
def test_isabs(self,input,output):
assert Path(input).isabs == output
def test_name(self, input, output):
assert Path(input).name == output
def test_suffixes(self,input,output):
assert Path(input).suffixes == output
def test_move_file(self):
file1 = File(self.root + '/tmp2.txt')
mv(file1, Path(self.root1 + '/tmp2.txt'))
file2 = File(self.root1 + '/tmp2.txt')
assert file2.exists and not file1.exists
def test_join_dot(self):
self.assertEqual((Path('.') / 'a').route, 'a')
def test_isroot(self,input,output):
assert Path(input).isroot == output
def test_father(self,input,output):
assert Path(input).father == output