def listmode_from_gate_out(path, scanner, nb_sub):
full_data = None
for i in tqdm(range(nb_sub)):
path_ = path.replace('?', str(i))
data = np.load(path_)[:, :7]
if full_data is None:
full_data = np.array(data)
else:
full_data = np.vstack((full_data, data))
if isinstance(scanner, nef.PetEcatScanner):
lors = Lors(full_data)
listmode = Listmode(np.ones((lors.length, ), dtype=np.float32), lors)
row = nef.EcatCrystalPosToIndex(scanner)(lors.data[:, :3])
col = nef.EcatCrystalPosToIndex(scanner)(lors.data[:, 3:])
lors_data1 = nef.EcatIndexToCrystalPos(scanner)(row)
lors_data2 = nef.EcatIndexToCrystalPos(scanner)(col)
lors = np.hstack((lors_data1, lors_data2))
return Listmode(np.ones((lors.shape[0], ), dtype=np.float32), lors)
elif isinstance(scanner, nef.PetCylindricalScanner):
lors = Lors(full_data)
listmode = Listmode(np.ones((lors.length, ), dtype=np.float32), lors)
ind1 = nef.CylindricalCrystalPosToIndex(scanner)(lors.data[:, :3])
ind2 = nef.CylindricalCrystalPosToIndex(scanner)(lors.data[:, 3:])
lors_data1 = nef.CylindricalIndexToCrystalPos(scanner)(ind1)
lors_data2 = nef.CylindricalIndexToCrystalPos(scanner)(ind2)
lors_data = np.hstack((lors_data1, lors_data2))
return listmode.update(lors=nef.Lors(lors_data))
else:
raise NotImplementedError
def __call__(self, sino: Sinogram) -> Listmode:
irow_, icol_ = sino.data.nonzero()
data_ = sino.data.data
pos1 = EcatIndexToCrystalPos(self.scanner)(irow_)
pos2 = EcatIndexToCrystalPos(self.scanner)(icol_)
lors_data = np.hstack((pos1, pos2))
return Listmode(data_, Lors(lors_data))
def listmode_tof_from_gate_out(path, scanner, nb_sub):
full_data = None
for i in tqdm(range(nb_sub)):
path_ = path.replace('?', str(i))
data = np.load(path_)[:, :7]
if full_data is None:
full_data = np.array(data)
else:
full_data = np.vstack((full_data, data))
lors = Lors(full_data)
listmode = Listmode(np.ones((lors.length, ), dtype=np.float32), lors)
row, col = ListmodeToId()(listmode, scanner)
lors = IdToListmode()(row, col, scanner)
print(lors.data.shape)
print(full_data.shape)
lors_tof = lors.update(
data=np.append(lors.data, full_data[:, -1].reshape(-1, 1), axis=1))
return Listmode(np.ones((lors.shape[0], ), dtype=np.float32), lors_tof)
def _load_data(self, key):
KC = self.KEYS.CONFIG
if key == KC.EMAP_PATH:
result = load(Emap, self.config.get(key))
else:
listmode = load(Listmode, self.config.get(key))
len_per_sub = listmode.data.shape[0] // self.nb_workers
tid = self.task_index
result = Listmode(
listmode.data[tid * len_per_sub:(tid + 1) * len_per_sub],
Lors(listmode.lors.data[tid * len_per_sub:(tid + 1) *
len_per_sub, :]))
return result
def __call__(self, listmode: Listmode) -> Listmode:
pos1 = listmode.lors.data[:, :3]
pos2 = listmode.lors.data[:, 3:6]
ind1 = CylindricalCrystalPosToIndex(self.scanner)(pos1)
ind2 = CylindricalCrystalPosToIndex(self.scanner)(pos2)
pos1_new = CylindricalIndexToCrystalPos(self.scanner)(ind1)
pos2_new = CylindricalIndexToCrystalPos(self.scanner)(ind2)
if listmode.lors.data.shape[1] == 6:
lors_data_new = np.hstack((pos1_new, pos2_new)).astype(np.float32)
else:
tof_val = listmode.lors.data[:, -1]
lors_data_new = np.hstack((pos1_new, pos2_new, tof_val.reshape(-1, 1))).astype(
np.float32)
return listmode.update(lors = Lors(lors_data_new))
def listmode_from_gate_out_multi_bed(path, scanner, nb_sub):
full_data = {}
for i in tqdm(range(nb_sub)):
path_ = path.replace('?', str(i))
data = np.load(path_)[:, :7]
bed_id = np.load(path_)[:, -1]
for i_bed in set(bed_id):
if i_bed not in full_data:
full_data[i_bed] = np.array(data[bed_id == i_bed, :])
else:
full_data[i_bed] = np.vstack(
(full_data[i_bed], data[bed_id == i_bed, :]))
listmode_out = {}
for key, values in full_data.items():
lors = Lors(values)
listmode = Listmode(np.ones((lors.length, ), dtype=np.float32), lors)
row, col = ListmodeToId()(listmode, scanner)
lors = IdToListmode()(row, col, scanner)
listmode_out[key] = Listmode(
np.ones((lors.shape[0], ), dtype=np.float32), lors)
return listmode_out
def __call__(self, listmodes: List(Listmode)) -> Listmode:
lors = Lors(np.vstack([lm.lors.data for lm in listmodes]))
listmode = Listmode(np.hstack([lm.data for lm in listmodes]), lors)
return listmode