From f65f050696be761ab637eaede2515f6c44fd9ee3 Mon Sep 17 00:00:00 2001 From: przebieglykaziu Date: Wed, 18 Mar 2020 21:02:37 -0400 Subject: [PATCH] minor fixes in RADCURE example --- imgtools/examples/radcure_simple.py | 8 ++++---- imgtools/pipeline.py | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/imgtools/examples/radcure_simple.py b/imgtools/examples/radcure_simple.py index e792b9a..78c4899 100644 --- 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 index b4dc60a..0636de5 100644 --- 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