updated, passing tests. Updated version to 0.4

bhklab · Jun 22, 2022 · 81d6795 · 81d6795
1 parent 13f90fd
commit 81d6795
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Showing 3 changed files with 15 additions and 10 deletions.
diff --git a/setup.py b/setup.py
@@ -8,8 +8,8 @@
 
 setup(
     name="med-imagetools",
-    version="0.2.3",
-    author="Michal Kazmierski, Sejin Kim, Vishwesh Ramanathan, Benjamin Haibe-Kains",
+    version="0.4",
+    author="Michal Kazmierski, Sejin Kim, Kevin Qu, Vishwesh Ramanathan, Benjamin Haibe-Kains",
     author_email="benjamin.haibe.kains@utoronto.ca",
     description="Transparent and reproducible image processing pipelines in Python.",
     long_description=long_description,
@@ -20,7 +20,7 @@
     extras_require={
         'debug': ['pyvis'],
     },
-    entry_points={'console_scripts': ['autopipe = imgtools.autopipeline:main', 'autotest = imgtools.autonew:main']},
+    entry_points={'console_scripts': ['autopipeline = imgtools.autopipeline:main',]},
     classifiers=[
         "Programming Language :: Python :: 3",
         "Operating System :: OS Independent",

diff --git a/tests/test_modalities.py b/tests/test_modalities.py
@@ -35,7 +35,7 @@ def modalities_path():
     path["PT"] = pathlib.Path(qc_path, "08-27-1885-CA ORL FDG TEP POS TX-94629/532790.000000-LOR-RAMLA-44600").as_posix()
     return path
 
-@pytest.mark.parametrize("modalities", ["RTDOSE"])#["CT", "RTSTRUCT", "RTDOSE", "PT"])
+@pytest.mark.parametrize("modalities", ["CT", "RTSTRUCT", "RTDOSE", "PT"])
 def test_modalities(modalities, modalities_path):
     path = modalities_path
     img = read_dicom_auto(path["CT"]).image

diff --git a/tests/test_pipeline.py b/tests/test_pipeline.py
@@ -58,11 +58,14 @@ def test_output(n_jobs, sample_input_output):
     pipeline = SimplePipelineTest(input_paths[0], output_paths[0], n_jobs)
     pipeline.run()
 
-    for input_file, output_file in zip(os.scandir(input_paths[0]), os.scandir(output_paths[0])):
-        assert os.path.exists(output_file.path)
-        test_output = sitk.GetArrayFromImage(sitk.ReadImage(output_file.path))
-        true_output = sitk.GetArrayFromImage(sitk.ReadImage(input_file.path))
+    input_dir, output_dir = input_paths[0], output_paths[0]
+
+    for input_file, output_file in zip(sorted(os.listdir(input_dir)), sorted(os.listdir(output_dir))):
+        assert os.path.exists(pathlib.Path(output_dir, output_file))
+        test_output = sitk.GetArrayFromImage(sitk.ReadImage(pathlib.Path(output_dir, output_file).as_posix()))
+        true_output = sitk.GetArrayFromImage(sitk.ReadImage(pathlib.Path(input_dir, input_file).as_posix()))
         assert np.allclose(test_output, true_output)
+        print('passed assert')
 
 
 class MultiInputPipelineTest(Pipeline):
@@ -97,6 +100,7 @@ def test_missing_handling(n_jobs, missing_strategy, sample_input_output):
     input_paths, output_paths = sample_input_output
     # simulate partial missing data
     os.remove(pathlib.Path(input_paths[0], "test0.nrrd").as_posix())
+    print(input_paths, output_paths)
 
     pipeline = MultiInputPipelineTest(input_paths[0],
                                       input_paths[1],
@@ -109,15 +113,16 @@ def test_missing_handling(n_jobs, missing_strategy, sample_input_output):
         assert len(w) == 1
         assert missing_strategy in str(w[-1].message)
 
+    print(os.listdir(input_paths[1]), os.listdir(output_paths[1]))
     if missing_strategy == "drop":
         assert all([
             not os.path.exists(pathlib.Path(output_paths[0], "test0.nrrd").as_posix()),
             not os.path.exists(pathlib.Path(output_paths[1], "test0.nrrd").as_posix())
         ])
     else:
         assert all([
-            not os.path.exists(pathlib.Path(output_paths[0], "test0.nrrd").as_posix()),
-            os.path.exists(pathlib.Path(output_paths[1], "test0.nrrd").as_posix())
+            not os.path.exists(pathlib.Path(output_paths[0], "test0.nii.gz").as_posix()),
+            os.path.exists(pathlib.Path(output_paths[1], "test0.nii.gz").as_posix())
         ])