# Arguments
"""
choice = 'Isokerays'
data_path = '/media/dios/dios2/3DHistoData'
arguments = arg.return_args(data_path, choice)
"""
dataset = '4mm'
arguments = parse(choice=dataset)
# Extract sample list
if arguments.GUI:
samples = os.listdir(arguments.data_path)
samples.sort()
# Use listbox (Result is saved in listbox.file_list)
listbox.GetFileSelection(arguments.data_path)
samples = [samples[i] for i in listbox.file_list]
# file_paths = find_image_paths(arguments.data_path, samples)
file_paths = [str(arguments.data_path / f) for f in samples]
file_paths = [file_paths[13]]
else:
search = ['*OA*', '*KP*']
#search = ['*Rec*']
file_paths = []
for term in search:
file_paths.extend(glob(str(arguments.data_path / term)))
file_paths.sort()
samples = [31]
file_paths = [file_paths[i] for i in samples]
# Create log
# Files
if arguments.n_subvolumes > 1:
arguments.save_path = arguments.save_path + '_' + str(
arguments.n_subvolumes) + 'subs'
files = []
for sub in range(arguments.n_subvolumes):
files.extend([
os.path.basename(f) for f in glob(arguments.image_path +
'/*sub' + str(sub) + '.h5')
])
elif arguments.GUI:
arguments.image_path = arguments.image_path + '_large'
# Use listbox (Result is saved in listbox.file_list)
listbox.GetFileSelection(arguments.image_path)
files = listbox.file_list
else:
arguments.image_path = arguments.image_path + '_large'
files = [
os.path.basename(f)
for f in glob(arguments.image_path + '/' + '*.h5')
]
# Print output to log file
os.makedirs(arguments.save_path, exist_ok=True)
os.makedirs(arguments.save_path + '/Logs', exist_ok=True)
sys.stdout = open(
arguments.save_path + '/Logs/' + 'optimization_log_' +
str(date.today()) + str(strftime("-%H%M")) + '.txt', 'w')
)
parser.add_argument('--segmentation',
type=str,
choices=['torch', 'kmeans', 'cntk', 'unet'],
default='unet')
parser.add_argument('--input_shape', type=tuple, default=(32, 1, 768, 448))
parser.add_argument('--listbox', type=bool, default=False)
parser.add_argument('--overnight', type=bool, default=False)
parser.add_argument('--completed', type=int, default=33)
parser.add_argument('--threshold', type=int, default=0.2)
parser.add_argument('--n_jobs', type=int, default=12)
args = parser.parse_args()
if args.listbox:
# Use listbox (Result is saved in listbox.file_list)
listbox.GetFileSelection(str(args.path))
# Return list of samples
file_list = os.listdir(args.path)
file_list.sort()
file_list = [file_list[i] for i in listbox.file_list]
# Use glob
else:
search = ['*OA*', '*KP*']
file_list = []
for term in search:
file_list.extend(glob(str(args.path / term)))
file_list.sort()
calculate_multiple(args, file_list, skip=args.completed)
