Bone app

examples/apps/ct_bone_seg_app/__init__.py

@@ -0,0 +1,8 @@
+import os
+import sys
+
+_current_dir = os.path.abspath(os.path.dirname(__file__))
+if sys.path and os.path.abspath(sys.path[0]) != _current_dir:
+    sys.path.insert(0, _current_dir)
+
+del _current_dir

examples/apps/ct_bone_seg_app/__main__.py

@@ -0,0 +1,4 @@
+from app import App
+
+if __name__ == "__main__":
+    App(do_run=True)

examples/apps/ct_bone_seg_app/app.py

@@ -0,0 +1,36 @@
+# Copyright 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.
+
+from ct_bone_operator import CtBoneOperator
+from dicom_to_mhd import DicomToMhd
+
+from monai.deploy.core import Application, resource
+
+
+@resource(cpu=1, gpu=1)
+class App(Application):
+    """This is a CT Bone application."""
+
+    name = "ct_bone_app"
+    description = "CT Bone segmentation app."
+    version = "0.1.0"
+
+    def compose(self):
+        """This application has two operators."""
+
+        dcm_to_mhd = DicomToMhd()
+        bone_op = CtBoneOperator()
+
+        self.add_flow(dcm_to_mhd, bone_op)
+
+
+if __name__ == "__main__":
+    App(do_run=True)

examples/apps/ct_bone_seg_app/ct_bone_operator.py

@@ -0,0 +1,50 @@
+# Copyright 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 os
+
+import monai.deploy.core as md
+from monai.deploy.core import DataPath, ExecutionContext, InputContext, IOType, Operator, OutputContext
+
+
+@md.input("image", DataPath, IOType.DISK)
+@md.output("image", DataPath, IOType.DISK)
+@md.env(pip_packages=["patchelf", "clcat"])
+class CtBoneOperator(Operator):
+    """This Operator implements CT Bone segmentation"""
+
+    def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
+
+        input_path = op_input.get().path
+        inputfile = ""
+
+        if input_path.is_dir():
+            inputfile = os.path.join(input_path, "intermediate_mhd_data.mhd")
+        elif input_path.is_file():
+            inputfile = str(input_path)
+        else:
+            raise IOError("Input path invalid from input context")
+
+        output_path = op_output.get().path
+        output_path.mkdir(parents=True, exist_ok=True)
+        outputfile = os.path.join(output_path, "bone_mask.mhd")
+
+        import clcat.ct_algos as cact
+
+        status = cact.ct_bone(inputfile, outputfile)
+
+        if input_path.is_dir():
+            os.remove(inputfile)
+            inputrawfile = os.path.join(input_path, "intermediate_mhd_data.raw")
+            os.remove(inputrawfile)
+
+        if status != 0:
+            raise Exception("Bone segmentation failed")

examples/apps/ct_bone_seg_app/dicom_to_mhd.py

@@ -0,0 +1,55 @@
+# Copyright 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 os
+
+import monai.deploy.core as md
+from monai.deploy.core import DataPath, ExecutionContext, InputContext, IOType, Operator, OutputContext
+
+
+@md.input("image", DataPath, IOType.DISK)
+@md.output("image", DataPath, IOType.DISK)
+@md.env(pip_packages=["SimpleITK==1.2.4"])
+class DicomToMhd(Operator):
+    """
+    If input is DICOM: This operator converts a dicom image to a mhd image
+    If input is MHD: This operator sets the output path to input path
+    """
+
+    def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
+
+        input_path = op_input.get().path
+        if input_path.is_dir():
+            import SimpleITK as SITK
+
+            current_file_dir = os.path.abspath(os.path.dirname(__file__))
+            op_output.set(DataPath(current_file_dir))
+            output_path = op_output.get().path
+
+            output_file_path = os.path.join(output_path, "intermediate_mhd_data.mhd")
+
+            reader = SITK.ImageSeriesReader()
+            dicom_names = reader.GetGDCMSeriesFileNames(str(input_path))
+            reader.SetFileNames(dicom_names)
+
+            fixed = reader.Execute()
+            SITK.WriteImage(fixed, output_file_path)
+        else:
+            if os.path.isfile(input_path):
+                extension = os.path.splitext(input_path)[1]
+                if extension == ".mhd":
+                    # Input path is a MHD file
+                    # Setting output folder as input folder
+                    op_output.set(DataPath(input_path))
+                else:
+                    raise IOError("Unsupported extension")
+            else:
+                raise IOError("Invalid input path")