Warn when neither --in-place nor --output-directory are specified

README.md

@@ -6,6 +6,10 @@ Dicognito is a [Python](https://www.python.org/) module and command-line utility
 Use it to anonymize one or more DICOM files belonging to one or any number of patients. Objects will remain grouped
 in their original patients, studies, and series.
 
+Anonymization causes significant attributes, such as identifiers, names, and
+addresses, to be replaced by new values. Dates and times will be shifted into the
+past, but their order will remain consistent within and across the files.
+
 The package is [available on pypi](https://pypi.org/project/dicognito/) and can be installed from the command line by typing
 
 ```
@@ -17,15 +21,22 @@ pip install dicognito
 Once installed, a `dicognito` command will be added to your Python scripts directory.
 You can run it on entire filesystem trees or a collection of files specified by glob like so:
 
+```bash
+# Recurse down the filesystem, anonymizing all found DICOM files.
+# Anonymized files will be placed in out-dir, named by new SOP
+# instance UID.
+dicognito --output-directory out-dir .
+
+# Anonymize all files in the current directory with the dcm extension
+# (-o is an alias for --output-directory).
+dicognito -o out-dir *.dcm
+
+# Anonymize all files in the current directory with the dcm extension
+# but overwrite the original files.
+# Note: repeatedly anonymizing the same files will cause date attributes
+# to move farther into the past.
+dicognito --in-place *.dcm
 ```
-dicognito . # recurses down the filesystem, anonymizing all found DICOM files
-dicognito *.dcm # anonymizes all files in the current directory with the dcm extension
-```
-
-Files will be anonymized in place, with significant attributes, such as identifiers, names, and
-addresses, replaced by random values. Dates and times will be shifted a random amount, but their
-order will remain consistent within and across the files.
-
 Get more help via `dicognito --help`.
 
 ## Anonymizing from within Python

src/dicognito/__main__.py

@@ -55,6 +55,11 @@ def main(main_args: Optional[Sequence[str]] = None) -> None:
  raise ValueError("Invalid log level: %s" % args.log_level)
  logging.basicConfig(format="", level=numeric_level)
 
+ if not args.in_place and not args.output_directory:
+ logging.warning(
+ "Neither --output-directory/-o nor --in-place were specified. This will be an error in the future."
+ )
+
  anonymizer = Anonymizer(id_prefix=args.id_prefix, id_suffix=args.id_suffix, seed=args.seed)
 
  pipeline = Pipeline()

src/dicognito/release_notes.md

@@ -1,3 +1,9 @@
+### Changed
+
+- If neither `--in-place` or `--output-directory`/`-o` are specified on the command line, a
+ warning will be printed. The anonymization will proceed as if `--in-place` were specified.
+ A future release will require that one of the options be specified.
+
 ### New
 
 - `--in-place` flag added to explicitly specify in place editing of source files. It's an error

tests/test_commandline.py

@@ -22,11 +22,19 @@ def setup_module(module):
  shutil.copytree(orig_dir, data_dir)
 
 
-def test_overwrite_files():
+def test_implicit_in_place_warns_but_anonymizes(caplog):
  test_name = get_test_name()
  orig_dataset = read_original_file(test_name, "p01_s01_s01_i01.dcm")
  assert "CompressedSamples^MR1" == orig_dataset.PatientName
 
+ run_dicognito(path_to(""))
+
+ log_record = [log for log in caplog.records if log.levelname == "WARNING"][0]
+ assert (
+ "Neither --output-directory/-o nor --in-place were specified. This will be an error in the future."
+ in log_record.getMessage()
+ )
+
  run_dicognito(path_to("p*"))
 
  anon_dataset = read_file(test_name, "p01_s01_s01_i01.dcm")
@@ -128,7 +136,7 @@ def test_non_dicom_files_logged_at_info(caplog):
  assert "CompressedSamples^MR1" == orig_dataset.PatientName
 
  set_log_level(caplog, logging.INFO)
- run_dicognito(path_to(""))
+ run_dicognito("--in-place", path_to(""))
  anon_dataset = read_file(test_name, "p01_s01_s01_i01.dcm")
  assert orig_dataset.PatientName != anon_dataset.PatientName
 
@@ -141,7 +149,7 @@ def test_burned_in_annotation_default(caplog):
  expected_warnings = {"Burned In Annotation is YES in " + path_to("burned_in_yes.dcm")}
 
  set_log_level(caplog, logging.WARNING)
- run_dicognito(path_to(""))
+ run_dicognito("--in-place", path_to(""))
 
  messages = {log.getMessage() for log in caplog.records if log.levelname == "WARNING"}
  assert messages == expected_warnings
@@ -155,7 +163,7 @@ def test_burned_in_annotation_unless_no(caplog):
  }
 
  set_log_level(caplog, logging.WARNING)
- run_dicognito(path_to(""), "--assume-burned-in-annotation", "unless-no")
+ run_dicognito("--in-place", path_to(""), "--assume-burned-in-annotation", "unless-no")
 
  messages = {log.getMessage() for log in caplog.records if log.levelname == "WARNING"}
  assert messages == expected_warnings
@@ -165,15 +173,15 @@ def test_burned_in_annotation_if_yes(caplog):
  expected_warnings = {"Burned In Annotation is YES in " + path_to("burned_in_yes.dcm")}
 
  set_log_level(caplog, logging.WARNING)
- run_dicognito(path_to(""), "--assume-burned-in-annotation", "if-yes")
+ run_dicognito("--in-place", path_to(""), "--assume-burned-in-annotation", "if-yes")
 
  messages = {log.getMessage() for log in caplog.records if log.levelname == "WARNING"}
  assert messages == expected_warnings
 
 
 def test_burned_in_annotation_never(caplog):
  set_log_level(caplog, logging.WARNING)
- run_dicognito(path_to(""), "--assume-burned-in-annotation", "never")
+ run_dicognito("--in-place", path_to(""), "--assume-burned-in-annotation", "never")
 
  messages = {log.getMessage() for log in caplog.records if log.levelname == "WARNING"}
  assert not messages
@@ -183,7 +191,7 @@ def test_burned_in_annotation_warn(caplog):
  expected_warnings = {"Burned In Annotation is YES in " + path_to("burned_in_yes.dcm")}
 
  set_log_level(caplog, logging.WARNING)
- run_dicognito(path_to(""), "--on-burned-in-annotation", "warn")
+ run_dicognito("--in-place", path_to(""), "--on-burned-in-annotation", "warn")
 
  messages = {log.getMessage() for log in caplog.records if log.levelname == "WARNING"}
  assert messages == expected_warnings
@@ -194,7 +202,7 @@ def test_burned_in_annotation_fail(caplog):
  expected_message = "Burned In Annotation is YES in " + input_file_name
 
  with pytest.raises(SystemExit):
- run_dicognito(path_to(""), "--on-burned-in-annotation", "fail")
+ run_dicognito("--in-place", path_to(""), "--on-burned-in-annotation", "fail")
 
  log_record = [log for log in caplog.records if log.levelname == "ERROR"][0]
  assert f"Error occurred while converting {input_file_name}. Aborting.\nError was:" in log_record.getMessage()