--- a
+++ b/code/DMACS.py
@@ -0,0 +1,57 @@
+import time
+import numpy as np, nibabel as nib, pandas as pd
+import tensorflow as tf
+from deepseg import *
+from p1processing import *
+from p2processing import *
+from meshfitting import *
+from motionEstimation import *
+from decimation import *
+
+""" Deployment parameters """
+FLAGS = tf.app.flags.FLAGS
+#tf.app.flags.DEFINE_integer('coreNo', 3, 'Number of CPUs.')
+#tf.app.flags.DEFINE_string('test_dir', '/vol/medic02/users/jduan/New_BRIDGE_Cases4',
+#                           'Path to the test set directory, under which images are organised in '
+#                           'subdirectories for each subject.')
+#tf.app.flags.DEFINE_string('model_path', '/vol/medic02/users/jduan/HHData/tensorflowFCNCodes/DeepRegionEdgeSegmentation'
+#                           '/saver/model/vgg_RE_network/vgg_RE_network.ckpt-50000', 'Path to the saved trained model.')
+#tf.app.flags.DEFINE_string('atlas_dir', '/vol/medic02/users/jduan/HHData/3Dshapes_new', 'Path to the atlas.')
+#tf.app.flags.DEFINE_string('param_dir', '/vol/medic02/users/jduan/myPatchMatch/par', 'Path to the registration parameters.')
+#tf.app.flags.DEFINE_string('template_dir', '/vol/medic02/users/jduan/myPatchMatch/template_wenzhe', 'Path to the template.')
+#tf.app.flags.DEFINE_string('template_PH', '/vol/medic02/users/jduan/myPatchMatch/vtks', 'Path to the template.')
+
+
+
+tf.app.flags.DEFINE_integer('coreNo', 8, 'Number of CPUs.')
+tf.app.flags.DEFINE_string('test_dir', '/data',
+                           'Path to the test set directory, under which images are organised in '
+                           'subdirectories for each subject.')
+tf.app.flags.DEFINE_string('model_path',  '/model/vgg_RE_network.ckpt-50000', 'Path to the saved trained model.')
+tf.app.flags.DEFINE_string('atlas_dir',  '/refs', 'Path to the atlas.')
+tf.app.flags.DEFINE_string('param_dir', '/par', 'Path to the registration parameters.')
+tf.app.flags.DEFINE_string('template_dir', '/vtks/1', 'Path to the template.')
+tf.app.flags.DEFINE_string('template_PH', '/vtks/2', 'Path to the template.')
+tf.app.flags.DEFINE_boolean('irtk', True, 'use irtk or not')
+
+if __name__ == '__main__':
+    
+        print('Start evaluating on the test set ...')
+        table_time = []
+        start_time = time.time()
+
+        deeplearningseg(FLAGS.model_path, FLAGS.test_dir, FLAGS.atlas_dir)
+                 
+        # multiatlasreg2D(FLAGS.test_dir, FLAGS.atlas_dir, FLAGS.param_dir, FLAGS.coreNo, True, FLAGS.irtk) # parallel, irtk
+
+        multiatlasreg3D(FLAGS.test_dir, FLAGS.atlas_dir, FLAGS.param_dir, FLAGS.coreNo, True, FLAGS.irtk) # parallel, irtk
+
+        meshCoregstration(FLAGS.test_dir, FLAGS.param_dir, FLAGS.template_dir, FLAGS.coreNo, True, False) # parallel, irtk
+
+        motionTracking(FLAGS.test_dir, FLAGS.param_dir, FLAGS.template_PH, FLAGS.coreNo, True) # parallel
+        
+        decimate(FLAGS.test_dir, FLAGS.coreNo, False) 
+
+        process_time = time.time() - start_time 
+        print('Including image I/O, CUDA resource allocation, '
+              'it took {:.3f}s in total for processing all the subjects).'.format(process_time))