ENH: Test PathList interface

dzenanz · Sep 30, 2024 · 3f45090 · 3f45090
1 parent 5627df0
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diff --git a/wrapping/test/CMakeLists.txt b/wrapping/test/CMakeLists.txt
@@ -69,3 +69,26 @@ itk_python_add_test(NAME PythonANTsGroupwiseBrainSlices
     -i DATA{${test_input_dir}/OASIS-TRT-20-19Slice121.nii.gz}
     -i DATA{${test_input_dir}/OASIS-TRT-20-20Slice121.nii.gz}
   )
+
+itk_python_add_test(NAME PythonANTsGroupwisePaths
+  TEST_DRIVER_ARGS
+  --compare
+    DATA{${test_baseline_dir}/PythonANTsGroupwiseBrainSlices.nrrd}
+    ${ITK_TEST_OUTPUT_DIR}/PythonANTsGroupwisePaths.nrrd
+    --compareIntensityTolerance 10
+    --compareRadiusTolerance 5
+    --compareNumberOfPixelsTolerance 2000
+  COMMAND PythonANTsGroupwisePaths.py
+    -o ${ITK_TEST_OUTPUT_DIR}/PythonANTsGroupwisePaths.nrrd
+    -i DATA{${test_input_dir}/OASIS-TRT-20-10Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-11Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-12Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-13Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-14Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-15Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-16Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-17Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-18Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-19Slice121.nii.gz}
+    -i DATA{${test_input_dir}/OASIS-TRT-20-20Slice121.nii.gz}
+  )
diff --git a/wrapping/test/PythonANTsGroupwisePaths.py b/wrapping/test/PythonANTsGroupwisePaths.py
@@ -0,0 +1,66 @@
+#==========================================================================
+#
+#   Copyright NumFOCUS
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#          https://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+#==========================================================================*/
+
+
+import itk
+import argparse
+
+parser = argparse.ArgumentParser(description="Python groupwise registration test.")
+parser.add_argument("-i", "--input-image", action="append", help="Input image(s)", required=True)
+parser.add_argument("-t", "--initial-template", required=False)
+parser.add_argument("-o", "--output-template", required=True)
+args = parser.parse_args()
+
+itk.auto_progress(2)
+
+first_image = itk.imread(args.input_image[0])
+
+PixelType = itk.template(first_image)[1][0]
+Dimension = first_image.GetImageDimension()
+ImageType = itk.Image[PixelType, Dimension]
+assert ImageType == type(first_image)
+TemplateImageType = itk.Image[itk.F, Dimension]
+
+gwr = itk.ANTSGroupwiseRegistration[ImageType, TemplateImageType, itk.F].New()
+# pairwise registration has different order of template parameters
+pwr = itk.ANTSRegistration[TemplateImageType, ImageType, itk.F].New()
+
+if args.initial_template is not None:
+    print(f"Reading initial template: {args.initial_template}")
+    initial_template = itk.imread(args.initial_template)
+    gwr.SetInitialTemplateImage(initial_template)
+
+gwr.SetPathList(args.input_image)
+gwr.SetIterations(4)
+gwr.SetGradientStep(0.2)
+
+pwr.SetTypeOfTransform("SyN")
+pwr.SetSynMetric("CC")
+pwr.SetSynIterations([100, 70, 50, 0])
+pwr.SetRandomSeed(30101983)  # improve reproducibility
+
+gwr.SetPairwiseRegistration(pwr)
+print(gwr)
+
+print("Performing groupwise registration. This will take a while...")
+gwr.Update()
+
+print(f"Writing resulting template image into file: {args.output_template}")
+itk.imwrite(gwr.GetOutput(), args.output_template, compression=False)
+
+print("Test finished")