Enh: Anonymisation at runtime (#113)

* Enable anon as a command line flag

* Add help to anon option.

CHANGELOG.md

@@ -1,5 +1,9 @@
 This document contains the Spec2nii release history in reverse chronological order.
 
+0.7.1 (WIP)
+--------------------------------
+- The --anon flag can be passed with any call to anonymise after writing files.
+
 0.7.0 (Saturday 5th August 2023)
 --------------------------------
 - Fixed a bug in Philips Classic DICOM orientations (supplementing the fixes to Enhanced DICOM in `0.6.11`)

spec2nii/anonymise.py

@@ -13,17 +13,18 @@
 from nifti_mrs.hdr_ext import Hdr_Ext
 
 
-def anon_nifti_mrs(args):
-    """Function for anonymising input NIfTI-MRS files.
+def anon_nifti_mrs(nifti_mrs_img, extra_keys=None, verbose=False):
+    """Function for anonymising an existing nifti-mrs object
 
-    :param args: Command line arguments parsed in spec2nii.py
-    :return: List of anonymised images
-    :rtype: [nib.nifti2.Nifti2Image,]
-    :return: List of output names
-    :rtype: [str,]
+    :param nifti_mrs_img: NIfTI-MRS object to anonymise
+    :type nifti_mrs_img: nifti_mrs.nifti_mrs.NIFTI_MRS
+    :param extra_keys: List of keys to explicitly remove, defaults to None
+    :type extra_keys: List, optional
+    :param verbose: Print verbose output, defaults to False
+    :type verbose: bool, optional
+    :return: Anonymised NIfTI-MRS object
+    :rtype: nifti_mrs.nifti_mrs.NIFTI_MRS
     """
-    # Load data
-    nifti_mrs_img = NIFTI_MRS(args.file)
 
     # Extract header extension
     hdr_ext = nifti_mrs_img.hdr_ext.to_dict()
@@ -38,8 +39,8 @@ def iter_json(in_dict):
         removed = {}
         for key, value in in_dict.items():
             # Explicitly set on command line
-            if args.remove\
-                    and key in args.remove:
+            if extra_keys\
+                    and key in extra_keys:
                 removed.update({key: value})
             # Standard defined
             elif key in standard_defined:
@@ -65,24 +66,39 @@ def iter_json(in_dict):
 
     anon_hdr, removed_dict = iter_json(hdr_ext)
 
-    if args.verbose:
+    if verbose:
         pp = pprint.PrettyPrinter(indent=4)
         print('\nThe following keys were removed:')
         pp.pprint(removed_dict)
         print('\nThe following keys were kept:')
         pp.pprint(anon_hdr)
 
     # Make new NIfTI-MRS image
-    anon_out = gen_nifti_mrs_hdr_ext(
+    return gen_nifti_mrs_hdr_ext(
         nifti_mrs_img[:],
         nifti_mrs_img.dwelltime,
         Hdr_Ext.from_header_ext(anon_hdr),
         affine=nifti_mrs_img.getAffine('voxel', 'world'))
 
+
+def anon_file(args):
+    """Function for anonymising NIfTI-MRS files stored on drive.
+
+    :param args: Command line arguments parsed in spec2nii.py
+    :return: List of anonymised images
+    :rtype: [nib.nifti2.Nifti2Image,]
+    :return: List of output names
+    :rtype: [str,]
+    """
+
     # Process output name.
     if args.fileout:
         fname_out = [args.fileout, ]
     else:
         fname_out = [args.file.with_suffix('').with_suffix('').name, ]
 
-    return [anon_out, ], fname_out
+    return [
+        anon_nifti_mrs(
+            NIFTI_MRS(args.file),
+            verbose=args.verbose,
+            extra_keys=args.remove), ], fname_out

spec2nii/spec2nii.py

@@ -47,7 +47,12 @@ def add_common_parameters(subparser):
                                    help="Override SpectrometerFrequency field with input(s). Input in MHz.")
             subparser.add_argument("--override_dwelltime", type=float,
                                    help="Override dwell time field with input. Input in seconds.")
+            subparser.add_argument(
+                '--anon',
+                action='store_true',
+                help="Create file without sensitive metadata. For greater control use spec2nii anon.")
             subparser.add_argument('--verbose', action='store_true')
+
             return subparser
 
         # Auto subcommand - heuristic ID of file type
@@ -234,7 +239,8 @@ def add_common_parameters(subparser):
                                  nifti1=False,
                                  override_nucleus=None,
                                  override_frequency=None,
-                                 override_dwelltime=None)
+                                 override_dwelltime=None,
+                                 anon=False)
 
         parser_dump = subparsers.add_parser('dump', help='Dump contents of headers from existing NIfTI-MRS file.')
         parser_dump.add_argument('file', help='NIfTI-MRS file', type=Path)
@@ -264,7 +270,8 @@ def add_common_parameters(subparser):
                                    override_nucleus=None,
                                    override_frequency=None,
                                    override_dwelltime=None,
-                                   verbose=False)
+                                   verbose=False,
+                                   anon=False)
 
         if len(sys.argv) == 1:
             parser.print_usage(sys.stderr)
@@ -284,6 +291,12 @@ def add_common_parameters(subparser):
 
         if self.imageOut:
             self.implement_overrides(args)
+
+            if args.anon:
+                from spec2nii.anonymise import anon_nifti_mrs
+                for idx, nifti_mrs_img in enumerate(self.imageOut):
+                    self.imageOut[idx] = anon_nifti_mrs(nifti_mrs_img, verbose=args.verbose)
+
             self.validate_output()
             self.write_output(args.json, args.nifti1)
             self.validate_write(args.verbose)
@@ -641,8 +654,8 @@ def varian(self, args):
 
     # Anonymise function
     def anon(self, args):
-        from spec2nii.anonymise import anon_nifti_mrs
-        self.imageOut, self.fileoutNames = anon_nifti_mrs(args)
+        from spec2nii.anonymise import anon_file
+        self.imageOut, self.fileoutNames = anon_file(args)
 
     # Dump function
     @staticmethod

tests/test_anon.py

@@ -52,3 +52,26 @@ def test_anon(tmp_path):
     assert 'PatientName' not in hdr_ext_a
     assert 'PatientSex' not in hdr_ext_a
     assert 'RepetitionTime' not in hdr_ext_a
+
+
+def test_inline_anon(tmp_path):
+    # Convert twix
+    subprocess.check_call(['spec2nii', 'twix',
+                           '-e', 'image',
+                           '-f', 'original',
+                           '-o', tmp_path,
+                           '-j', str(data_path),
+                           '--anon',
+                           '--verbose'])
+
+    img_o = read_nifti_mrs(tmp_path / 'original.nii.gz')
+
+    hdr_ext_codes = img_o.header.extensions.get_codes()
+    hdr_ext_o = json.loads(img_o.header.extensions[hdr_ext_codes.index(44)].get_content())
+
+    assert 'SpectrometerFrequency' in hdr_ext_o
+    assert 'ResonantNucleus' in hdr_ext_o
+    assert 'dim_5' in hdr_ext_o
+    assert 'OriginalFile' not in hdr_ext_o
+    assert 'PatientName' not in hdr_ext_o
+    assert 'PatientDoB' not in hdr_ext_o