--- a
+++ b/luna_test_patient_segment.py
@@ -0,0 +1,59 @@
+import os
+import numpy as np
+import data_transforms
+import pathfinder
+import utils
+import utils_lung
+from configuration import set_configuration, config
+from utils_plots import plot_slice_3d_2, plot_2d, plot_2d_4, plot_slice_3d_3
+import utils_lung
+import lung_segmentation
+
+set_configuration('configs_seg_scan', 'luna_s_local')
+
+p_transform = {'patch_size': (416, 416, 416),
+               'mm_patch_size': (416, 416, 416),
+               'pixel_spacing': (1., 1., 1.)
+               }
+
+
+def test_luna3d():
+    image_dir = utils.get_dir_path('analysis', pathfinder.METADATA_PATH)
+    image_dir = image_dir + '/test_luna/'
+    utils.auto_make_dir(image_dir)
+
+    id2zyxd = utils_lung.read_luna_annotations(pathfinder.LUNA_LABELS_PATH)
+
+    luna_data_paths = [
+        'problem_patients/1.3.6.1.4.1.14519.5.2.1.6279.6001.877026508860018521147620598474.mhd']
+
+    candidates = utils.load_pkl(
+        'problem_patients/1.3.6.1.4.1.14519.5.2.1.6279.6001.877026508860018521147620598474.pkl')
+
+    candidates = candidates[:4]
+    print candidates
+    print '--------------'
+    print id2zyxd['1.3.6.1.4.1.14519.5.2.1.6279.6001.877026508860018521147620598474']
+
+    for k, p in enumerate(luna_data_paths):
+        id = os.path.basename(p).replace('.mhd', '')
+        print id
+        img, origin, pixel_spacing = utils_lung.read_mhd(p)
+        lung_mask = lung_segmentation.segment_HU_scan_elias(img)
+        x, annotations_tf, tf_matrix, lung_mask_out = data_transforms.transform_scan3d(data=img,
+                                                                                       pixel_spacing=pixel_spacing,
+                                                                                       p_transform=p_transform,
+                                                                                       luna_annotations=candidates,
+                                                                                       p_transform_augment=None,
+                                                                                       luna_origin=origin,
+                                                                                       lung_mask=lung_mask,
+                                                                                       world_coord_system=False)
+
+        for zyxd in annotations_tf:
+            plot_slice_3d_2(x, lung_mask_out, 0, id, img_dir='./', idx=zyxd)
+            plot_slice_3d_2(x, lung_mask_out, 1, id, img_dir='./', idx=zyxd)
+            plot_slice_3d_2(x, lung_mask_out, 2, id, img_dir='./', idx=zyxd)
+
+
+if __name__ == '__main__':
+    test_luna3d()