Merge pull request #361 from Project-MONAI/vikash/nii_loader

Added a Nifti data loader for issue #270

Author: GreySeaWolf

monai/deploy/operators/__init__.py

@@ -30,6 +30,7 @@
     PublisherOperator
     STLConversionOperator
     STLConverter
+    NiftiDataLoader
 """
 
 from .clara_viz_operator import ClaraVizOperator
@@ -43,6 +44,7 @@
 from .inference_operator import InferenceOperator
 from .monai_bundle_inference_operator import BundleConfigNames, IOMapping, MonaiBundleInferenceOperator
 from .monai_seg_inference_operator import MonaiSegInferenceOperator
+from .nii_data_loader_operator import NiftiDataLoader
 from .png_converter_operator import PNGConverterOperator
 from .publisher_operator import PublisherOperator
 from .stl_conversion_operator import STLConversionOperator, STLConverter

monai/deploy/operators/nii_data_loader_operator.py

@@ -0,0 +1,53 @@
+# Copyright 2021-2022 MONAI Consortium
+# 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
+#     http://www.apache.org/licenses/LICENSE-2.0
+# 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 numpy as np
+import SimpleITK
+
+import monai.deploy.core as md
+from monai.deploy.core import DataPath, ExecutionContext, InputContext, IOType, Operator, OutputContext
+
+
+@md.input("image_path", DataPath, IOType.DISK)
+@md.output("image", np.ndarray, IOType.IN_MEMORY)
+class NiftiDataLoader(Operator):
+    """
+    This operator reads a nifti image, extracts the numpy array and forwards it to the next operator
+    """
+
+    def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
+        input_path = op_input.get().path
+        image_np = self.convert_and_save(input_path)
+        op_output.set(image_np)
+
+    def convert_and_save(self, nii_path):
+        """
+        reads the nifti image and
+        """
+        image_reader = SimpleITK.ImageFileReader()
+        image_reader.SetFileName(str(nii_path))
+        image = image_reader.Execute()
+        image_np = np.transpose(SimpleITK.GetArrayFromImage(image), [2, 1, 0])
+        return image_np
+
+
+def test():
+    filepath = "/home/gupta/Documents/mni_icbm152_nlin_sym_09a/mni_icbm152_gm_tal_nlin_sym_09a.nii"
+    nii_operator = NiftiDataLoader()
+    image_np = nii_operator.convert_and_save(filepath)
+
+
+def main():
+    test()
+
+
+if __name__ == "__main__":
+    main()