CT Bone operator updated with clcat pypi package

Author: shekhardw

examples/apps/ct_bone_seg_app/__init__.py

@@ -4,6 +4,5 @@
 _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)
-    #lib_path = os.path.join(_current_dir, "lib/")
-    #sys.path.insert(0, lib_path)
+
 del _current_dir

examples/apps/ct_bone_seg_app/app.py

@@ -1,4 +1,4 @@
-# Copyright 2021 MONAI Consortium
+# 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
@@ -14,24 +14,16 @@
 from monai.deploy.core import Application, env, resource
 
 @resource(cpu=1, gpu=1)
-# pip_packages can be a string that is a path(str) to requirements.txt file or a list of packages.
-#@env(pip_packages=["scikit-image >= 0.17.2"])
 class App(Application):
     """This is a CT Bone application.
     """
 
-    # App's name. <class name>('App') if not specified.
     name = "ct_bone_app"
-    # App's description. <class docstring> if not specified.
     description = "CT Bone segmentation app."
-    # App's version. <git version tag> or '0.0.0' if not specified.
     version = "0.1.0"
 
     def compose(self):
         """This application has two operators.
-
-        Each operator has a single input and a single output port.
-        Each operator performs some kind of image processing function.
         """
 
         dcm_to_mhd = DicomToMhd()

examples/apps/ct_bone_seg_app/ct_bone_operator.py

@@ -1,4 +1,4 @@
-# Copyright 2021 MONAI Consortium
+# 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
@@ -11,20 +11,13 @@
 
 import monai.deploy.core as md
 from monai.deploy.core import DataPath, ExecutionContext, Image, InputContext, IOType, Operator, OutputContext
-import sys, os
-
-lib_path = "/usr/local/lib"
-sys.path.append(lib_path)
-import clinical_algos as calg
-
+import os
 
 @md.input("image", DataPath, IOType.DISK)
 @md.output("image", DataPath, IOType.DISK)
-# If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
-# operators and the application in packaging time.
-# @md.env(pip_packages=["scikit-image >= 0.17.2"])
+@md.env(pip_packages=["patchelf", "clcat"])
 class CtBoneOperator(Operator):
-    """This Operator implements a CT Bone segmentation
+    """This Operator implements CT Bone segmentation
     """
 
     def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
@@ -36,17 +29,15 @@ def compute(self, op_input: InputContext, op_output: OutputContext, context: Exe
             inputfile = os.path.join(input_path, "intermediate_mhd_data.mhd")
         elif input_path.is_file():
             inputfile = str(input_path)
-        
-        print(inputfile)
+        else:
+            raise("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")
-        print(outputfile)
-
-        print("Entering Clara CAT Algorithms")
 
-        status = calg.ct_bone(inputfile, outputfile)
+        import clcat.ct_algos as cact
+        status = cact.ct_bone(inputfile, outputfile)
 
         if input_path.is_dir():
             os.remove(inputfile)

examples/apps/ct_bone_seg_app/dicom_to_mhd.py

@@ -1,4 +1,4 @@
-# Copyright 2021 MONAI Consortium
+# 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
@@ -16,8 +16,6 @@
 
 @md.input("image", DataPath, IOType.DISK)
 @md.output("image", DataPath, IOType.DISK)
-# If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
-# operators and the application in packaging time.
 @md.env(pip_packages=["SimpleITK==1.2.4"])
 class DicomToMhd(Operator):
     """
@@ -29,12 +27,9 @@ def compute(self, op_input: InputContext, op_output: OutputContext, context: Exe
 
         input_path = op_input.get().path
         if input_path.is_dir():
-            print(input_path)
-            _current_dir = os.path.abspath(os.path.dirname(__file__))
-            op_output.set(DataPath(_current_dir))
+            current_file_dir = os.path.abspath(os.path.dirname(__file__))
+            op_output.set(DataPath(current_file_dir))
             output_path = op_output.get().path
-            if output_path.is_dir():
-                print(output_path)
 
             output_file_path = os.path.join(output_path, "intermediate_mhd_data.mhd")
 
@@ -45,12 +40,11 @@ def compute(self, op_input: InputContext, op_output: OutputContext, context: Exe
             fixed = reader.Execute()
             sitk.WriteImage(fixed, output_file_path)
         else:
-            print("Input path is not a directory")
             if os.path.isfile(input_path):
                 extension = os.path.splitext(input_path)[1]
                 if extension == '.mhd':
-                    print("Input path is a MHD file")
-                    print("Setting output folder as input folder")
+                    # Input path is a MHD file
+                    # Setting output folder as input folder
                     op_output.set(DataPath(input_path))
                 else:
                     raise IOError('Unsupported extension')