--- a
+++ b/options.py
@@ -0,0 +1,137 @@
+import argparse
+import os
+
+import torch
+
+### Parser
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--dataroot', default='./data/TCGA_GBMLGG', help="datasets")
+    parser.add_argument('--checkpoints_dir', type=str, default='./checkpoints/TCGA_GBMLGG', help='models are saved here')
+    parser.add_argument('--exp_name', type=str, default='exp_name', help='name of the project. It decides where to store samples and models')
+    parser.add_argument('--gpu_ids', type=str, default='0', help='gpu ids: e.g. 0  0,1,2, 0,2. use -1 for CPU')
+    parser.add_argument('--mode', type=str, default='omic', help='mode')
+    parser.add_argument('--model_name', type=str, default='omic', help='mode')
+    parser.add_argument('--use_vgg_features', type=int, default=0, help='Use pretrained embeddings')
+    parser.add_argument('--use_rnaseq', type=int, default=0, help='Use RNAseq data.')
+    
+    parser.add_argument('--task', type=str, default='surv', help='surv | grad')
+    parser.add_argument('--useRNA', type=int, default=0) # Doesn't work at the moment...:(
+    parser.add_argument('--useSN', type=int, default=1)
+    parser.add_argument('--act_type', type=str, default='Sigmoid', help='activation function')
+    parser.add_argument('--input_size_omic', type=int, default=80, help="input_size for omic vector")
+    parser.add_argument('--input_size_path', type=int, default=512, help="input_size for path images")
+    parser.add_argument('--init_gain', type=float, default=0.02, help='scaling factor for normal, xavier and orthogonal.')
+    parser.add_argument('--save_at', type=int, default=20, help="adsfasdf")
+    parser.add_argument('--label_dim', type=int, default=1, help='size of output')
+    parser.add_argument('--measure', default=1, type=int, help='disables measure while training (make program faster)')
+    parser.add_argument('--verbose', default=1, type=int)
+    parser.add_argument('--print_every', default=0, type=int)
+
+    parser.add_argument('--optimizer_type', type=str, default='adam')
+    parser.add_argument('--beta1', type=float, default=0.9, help='0.9, 0.5 | 0.25 | 0')
+    parser.add_argument('--beta2', type=float, default=0.999, help='0.9, 0.5 | 0.25 | 0')
+    parser.add_argument('--lr_policy', default='linear', type=str, help='5e-4 for Adam | 1e-3 for AdaBound')
+    parser.add_argument('--finetune', default=1, type=int, help='5e-4 for Adam | 1e-3 for AdaBound')
+    parser.add_argument('--final_lr', default=0.1, type=float, help='Used for AdaBound')
+    parser.add_argument('--reg_type', default='omic', type=str, help="regularization type")
+    parser.add_argument('--niter', type=int, default=0, help='# of iter at starting learning rate')
+    parser.add_argument('--niter_decay', type=int, default=25, help='# of iter to linearly decay learning rate to zero')
+    parser.add_argument('--epoch_count', type=int, default=1, help='start of epoch')
+    parser.add_argument('--batch_size', type=int, default=32, help="Number of batches to train/test for. Default: 256")
+
+    parser.add_argument('--lambda_cox', type=float, default=1)
+    parser.add_argument('--lambda_reg', type=float, default=3e-4)
+    parser.add_argument('--lambda_nll', type=float, default=1)
+
+
+    parser.add_argument('--fusion_type', type=str, default="pofusion", help='concat | pofusion')
+    parser.add_argument('--skip', type=int, default=0)
+    parser.add_argument('--use_bilinear', type=int, default=1)
+    parser.add_argument('--path_gate', type=int, default=1)
+    parser.add_argument('--grph_gate', type=int, default=1)
+    parser.add_argument('--omic_gate', type=int, default=1)
+    parser.add_argument('--path_dim', type=int, default=32)
+    parser.add_argument('--grph_dim', type=int, default=32)
+    parser.add_argument('--omic_dim', type=int, default=32)
+    parser.add_argument('--path_scale', type=int, default=1)
+    parser.add_argument('--grph_scale', type=int, default=1)
+    parser.add_argument('--omic_scale', type=int, default=1)
+    parser.add_argument('--mmhid', type=int, default=64)
+
+    parser.add_argument('--init_type', type=str, default='none', help='network initialization [normal | xavier | kaiming | orthogonal | max]. Max seems to work well')
+    parser.add_argument('--dropout_rate', default=0.25, type=float, help='0 - 0.25. Increasing dropout_rate helps overfitting. Some people have gone as high as 0.5. You can try adding more regularization')
+    parser.add_argument('--use_edges', default=1, type=float, help='Using edge_attr')
+    parser.add_argument('--pooling_ratio', default=0.2, type=float, help='pooling ratio for SAGPOOl')
+    parser.add_argument('--lr', default=2e-3, type=float, help='5e-4 for Adam | 1e-3 for AdaBound')
+    parser.add_argument('--weight_decay', default=4e-4, type=float, help='Used for Adam. L2 Regularization on weights. I normally turn this off if I am using L1. You should try')
+    parser.add_argument('--GNN', default='GCN', type=str, help='GCN | GAT | SAG. graph conv mode for pooling')
+    parser.add_argument('--patience', default=0.005, type=float)
+    opt = parser.parse_known_args()[0]
+    print_options(parser, opt)
+    opt = parse_gpuids(opt)
+    return opt
+
+
+def print_options(parser, opt):
+    """Print and save options
+
+    It will print both current options and default values(if different).
+    It will save options into a text file / [checkpoints_dir] / opt.txt
+    """
+    message = ''
+    message += '----------------- Options ---------------\n'
+    for k, v in sorted(vars(opt).items()):
+        comment = ''
+        default = parser.get_default(k)
+        if v != default:
+            comment = '\t[default: %s]' % str(default)
+        message += '{:>25}: {:<30}{}\n'.format(str(k), str(v), comment)
+    message += '----------------- End -------------------'
+    print(message)
+
+    # save to the disk
+    expr_dir = os.path.join(opt.checkpoints_dir, opt.exp_name, opt.model_name)
+    mkdirs(expr_dir)
+    file_name = os.path.join(expr_dir, '{}_opt.txt'.format('train'))
+    with open(file_name, 'wt') as opt_file:
+        opt_file.write(message)
+        opt_file.write('\n')
+
+
+def parse_gpuids(opt):
+    # set gpu ids
+    str_ids = opt.gpu_ids.split(',')
+    opt.gpu_ids = []
+    for str_id in str_ids:
+        id = int(str_id)
+        if id >= 0:
+            opt.gpu_ids.append(id)
+    if len(opt.gpu_ids) > 0:
+        torch.cuda.set_device(opt.gpu_ids[0])
+
+    return opt
+
+
+def mkdirs(paths):
+    """create empty directories if they don't exist
+
+    Parameters:
+        paths (str list) -- a list of directory paths
+    """
+    if isinstance(paths, list) and not isinstance(paths, str):
+        for path in paths:
+            mkdir(path)
+    else:
+        mkdir(paths)
+
+
+def mkdir(path):
+    """create a single empty directory if it didn't exist
+
+    Parameters:
+        path (str) -- a single directory path
+    """
+    if not os.path.exists(path):
+        os.makedirs(path)