add comments and normalized the ct image

fortex/health/readers/CT_image_reader.py

@@ -1,4 +1,4 @@
-# Copyright 2022 The Forte Authors. All Rights Reserved.
+# Copyright 2023 The Forte Authors. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -12,9 +12,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """
-This class is designed to read CT images from given folder path.
+This class is designed to read all CT images from given folder path.
 For more information for the dataset, visit:
-https://data.mendeley.com/datasets/jctsfj2sfn/1
+https://www.kaggle.com/competitions/rsna-str-pulmonary-embolism-detection/data
 """
 import os
 from typing import Iterator, List
@@ -25,7 +25,7 @@
 
 
 class CTimageReader(PackReader):
-    r""":class:`CTimageReader` is designed to read CT image files from a given folder."""
+    r""":class:`CTimageReader` is designed to read CT image files from a given folder path."""
 
     def _collect(self, image_directory) -> Iterator[List]:
         r"""Should be called with param ``image_directory`` which is a path to a
@@ -46,25 +46,29 @@ def _parse_pack(self, file_path: str) -> Iterator[DataPack]:
 
         # Read in image data and store in DataPack
         img = pydicom.dcmread(file_path, **(self.configs.read_kwargs or {}))
+        # YBR_FULL allows to read pixels in raw format without any compression
         img.PhotometricInterpretation = "YBR_FULL"
         pixel_data = img.pixel_array
-        pack.add_image(image=pixel_data)
+        slope=img[('0028','1052')].value
+        intercept=img[('0028','1052')].value
+        normalized_image=(img*slope +intercept)
+        pack.add_image(image=normalized_image)
         pack.pack_name = file_path.split("/")[-1]
 
         yield pack
 
     @classmethod
     def default_configs(cls):
-        r"""This defines a basic configuration structure for image reader.
+        r"""This defines a basic configuration structure for CT image reader.
 
         Here:
 
-          - file_ext (str): The file extension to find the target audio files
-             under a specific directory path. Default value is ".jpeg".
+          - file_ext (str): The file extension to find the target CT image files
+             under a specific directory path. Default value is ".dcm".
 
           - read_kwargs (dict): A dictionary containing all the keyword
-             arguments for `PIL.Image` method. For details, refer to
-             https://pillow.readthedocs.io/en/stable/reference/Image.html
+             arguments for `pydicom.dcmread` method. For details, refer to
+             https://pydicom.github.io/pydicom/stable/
              Default value is None.
 
         Returns: The default configuration of Image reader.