Skim2257 quick fix (#26)

* Updated crawler to force String on all meta fields

* Update setup.py

Former-commit-id: e942f7e [formerly d83fb0135155c4c94846c23614e75805db63cf37] [formerly 5e93381]
Former-commit-id: 65d66d2
Former-commit-id: 8a58ea10fb3416e01953eea428dac12e97f2fb8f

imgtools/utils/crawl.py

@@ -18,10 +18,10 @@ def crawl_one(folder):
         # instance (slice) information
         for dcm in dicoms:
             meta = dcmread(dcm)
-            patient  = meta.PatientID
-            study    = meta.StudyInstanceUID
-            series   = meta.SeriesInstanceUID
-            instance = meta.SOPInstanceUID
+            patient  = str(meta.PatientID)
+            study    = str(meta.StudyInstanceUID)
+            series   = str(meta.SeriesInstanceUID)
+            instance = str(meta.SOPInstanceUID)
 
             reference_ct, reference_rs, reference_pl = " ", " ", " "
             try: #RTSTRUCT
@@ -136,4 +136,4 @@ def crawl(top,
 
     args = parser.parse_args()
     db = crawl(args.directory, n_jobs=args.n_jobs)
-    print("# patients:", len(db))
+    print("# patients:", len(db))

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="med-imagetools",
-    version="0.2.2",
+    version="0.2.3",
     author="Michal Kazmierski, Sejin Kim, Vishwesh Ramanathan, Benjamin Haibe-Kains",
     author_email="benjamin.haibe.kains@utoronto.ca",
     description="Transparent and reproducible image processing pipelines in Python.",