Additional improvements to charactarize_data script

Changed the way the file list of images comprising a DICOM series is
returned. Previously they were returned in random order, this change
ensures that they are returned in the order that enables the
SeriesImageReader to read the image from the dataframe contents
without additional computations.

Author: zivy

Python/scripts/characterize_data.py

@@ -373,34 +373,48 @@ def inspect_single_series(series_data, meta_data_info={}, thumbnail_settings={})
         reader = sitk.ImageSeriesReader()
         reader.MetaDataDictionaryArrayUpdateOn()
         reader.LoadPrivateTagsOn()
-        # CHANGE to split list of tag values and sid is first entry
+        # split list of tag values, sid is first entry (see inspect_series)
         sid = series_data[0].split(":")[0]
         file_names = series_info["files"]
-        # As the files comprising a series with multiple files can reside in
-        # separate directories and SimpleITK expects them to be in a single directory
+        # As the files comprising a series can reside in separate directories
+        # and may have identical file names (e.g. 1/Z0.dcm, 2/Z0.dcm)
         # we use a tempdir and symbolic links to enable SimpleITK to read the series as
-        # a single image. Additionally, the files are renamed as they may have resided in
-        # separate directories with the same file name. Finally, on Windows
-        # we need to copy the files to the tempdir as the os.symlink documentation says that
+        # a single image (ImageSeriesReader_GetGDCMSeriesFileNames expects all files to
+        # be in a single directory).
+        # On Windows we need to copy the files to the tempdir as the os.symlink documentation says that
         # "On newer versions of Windows 10, unprivileged accounts can create symlinks
         # if Developer Mode is enabled. When Developer Mode is not available/enabled,
         # the SeCreateSymbolicLinkPrivilege privilege is required, or the process must be
         # run as an administrator."
         # To turn Developer Mode on in Windows 11:
         # Settings->System->For Developers and turn Developer Mode on.
-        # We could then comment out the Windows specific code below.
+        # We could then use the os.symlink function instead of the indirect usage of a
+        # copy_link_function below.
         with tempfile.TemporaryDirectory() as tmpdirname:
-            if platform.system() == "Windows":
-                for i, fname in enumerate(file_names):
-                    shutil.copy(
-                        os.path.abspath(fname), os.path.join(tmpdirname, str(i))
-                    )
-            else:
-                for i, fname in enumerate(file_names):
-                    os.symlink(os.path.abspath(fname), os.path.join(tmpdirname, str(i)))
-            reader.SetFileNames(
-                sitk.ImageSeriesReader_GetGDCMSeriesFileNames(tmpdirname, sid)
+            copy_link_function = (
+                shutil.copy if platform.system() == "Windows" else os.symlink
             )
+            new_orig_file_name_dict = {}
+            for i, fname in enumerate(file_names):
+                new_fname = os.path.join(tmpdirname, str(i))
+                new_orig_file_name_dict[new_fname] = fname
+                copy_link_function(fname, new_fname)
+            # For some reason on windows the returned full paths use double backslash
+            # for all directories except the last one which has a slash. This does not
+            # match the contents of the new_orig_file_name_dict which has a backslash
+            # for the last entry too. In the code below we call os.path.normpath to
+            # address this issue.
+            sorted_new_file_names = sitk.ImageSeriesReader_GetGDCMSeriesFileNames(
+                tmpdirname, sid
+            )
+            # store the file names in a sorted order so that they are saved in this
+            # manner. This is useful for reading from the saved csv file
+            # using the SeriesImageReader or ImageRead which expect ordered file names
+            series_info["files"] = [
+                new_orig_file_name_dict[os.path.normpath(new_fname)]
+                for new_fname in sorted_new_file_names
+            ]
+            reader.SetFileNames(sorted_new_file_names)
             img = reader.Execute()
             for k in meta_data_info.values():
                 if reader.HasMetaDataKey(0, k):