minor fixes in RADCURE example

bhklab · Mar 19, 2020 · f65f050 · f65f050
1 parent 8f93220
commit f65f050
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/imgtools/examples/radcure_simple.py b/imgtools/examples/radcure_simple.py
@@ -15,8 +15,8 @@ class RADCUREPipeline(Pipeline):
     """
 
     def __init__(self,
-                 input_directory="/cluster/projects/radiomics/RADCURE-images/",
-                 output_directory="./RADCURE-processed",
+                 input_directory,
+                 output_directory=,
                  spacing=(1., 1., 0.),
                  n_jobs=-1,
                  missing_strategy="drop",
@@ -44,7 +44,7 @@ def __init__(self,
             ImageFileLoader(
                 self.input_directory,
                 get_subject_id_from="subject_directory",
-                subdir_path="*/structures",
+                subdir_path="*/structures/RTSTRUCT.dcm",
                 reader=read_dicom_rtstruct))
 
         # image processing ops
@@ -108,7 +108,7 @@ def process_one_subject(self, subject_id):
     parser.add_argument(
         "--n_jobs",
         type=int,
-        default=0,
+        default=1,
         help="The number of parallel processes to use.")
     parser.add_argument(
         "--show_progress",

diff --git a/imgtools/pipeline.py b/imgtools/pipeline.py
@@ -14,7 +14,7 @@ class Pipeline:
     the `process_one_case` method, which defines the processing steps for one
     case (i.e. one subject_id from data loaders).
     """
-    def __init__(self, n_jobs=0, missing_strategy="drop", show_progress=True):
+    def __init__(self, n_jobs=1, missing_strategy="drop", show_progress=True):
         """Initialize the base class.
 
         Parameters