Fix extra metadata defaults (#54)

* Add and set extra metadata default values correctly

* Add new and adapt existing tests

* Bump version

HISTORY.md

@@ -1,5 +1,9 @@
 # History
 
+## 0.5.1 (2021-10-04)
+
+* Fix default values for extra metadata fields
+
 ## 0.5.0 (2021-10-01)
 
 * Added extra metadata fields to PanImg object

panimg/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.5.0"
+__version__ = "0.5.1"
 
 import logging
 

panimg/models.py

@@ -47,6 +47,7 @@ class PatientSex(str, Enum):
     MALE = "M"
     FEMALE = "F"
     OTHER = "O"
+    EMPTY = ""
 
 
 DICOM_VR_TO_VALIDATION_REGEXP = {
@@ -66,6 +67,7 @@ class ExtraMetaData(NamedTuple):
     keyword: str  # DICOM tag keyword (eg. 'PatientID')
     vr: str  # DICOM Value Representation (eg. 'LO')
     field_name: str  # Name of field on PanImg model (eg. 'patient_id')
+    default_value: Any  # Default value for field
 
     @property
     def match_pattern(self):
@@ -99,16 +101,16 @@ def validate_metadata_value(*, key, value):
 
 
 EXTRA_METADATA = (
-    ExtraMetaData("PatientID", "LO", "patient_id"),
-    ExtraMetaData("PatientName", "PN", "patient_name"),
-    ExtraMetaData("PatientBirthDate", "DA", "patient_birth_date"),
-    ExtraMetaData("PatientAge", "AS", "patient_age"),
-    ExtraMetaData("PatientSex", "CS", "patient_sex"),
-    ExtraMetaData("StudyDate", "DA", "study_date"),
-    ExtraMetaData("StudyInstanceUID", "UI", "study_instance_uid"),
-    ExtraMetaData("SeriesInstanceUID", "UI", "series_instance_uid"),
-    ExtraMetaData("StudyDescription", "LO", "study_description"),
-    ExtraMetaData("SeriesDescription", "LO", "series_description"),
+    ExtraMetaData("PatientID", "LO", "patient_id", ""),
+    ExtraMetaData("PatientName", "PN", "patient_name", ""),
+    ExtraMetaData("PatientBirthDate", "DA", "patient_birth_date", None),
+    ExtraMetaData("PatientAge", "AS", "patient_age", ""),
+    ExtraMetaData("PatientSex", "CS", "patient_sex", ""),
+    ExtraMetaData("StudyDate", "DA", "study_date", None),
+    ExtraMetaData("StudyInstanceUID", "UI", "study_instance_uid", ""),
+    ExtraMetaData("SeriesInstanceUID", "UI", "series_instance_uid", ""),
+    ExtraMetaData("StudyDescription", "LO", "study_description", ""),
+    ExtraMetaData("SeriesDescription", "LO", "series_description", ""),
 )
 
 
@@ -128,16 +130,16 @@ class PanImg:
     window_width: Optional[float]
     color_space: ColorSpace
     eye_choice: EyeChoice
-    patient_id: Optional[str]
-    patient_name: Optional[str]
-    patient_birth_date: Optional[datetime.date]
-    patient_age: Optional[str]
-    patient_sex: Optional[PatientSex]
-    study_date: Optional[datetime.date]
-    study_instance_uid: Optional[str]
-    series_instance_uid: Optional[str]
-    study_description: Optional[str]
-    series_description: Optional[str]
+    patient_id: str = ""
+    patient_name: str = ""
+    patient_birth_date: Optional[datetime.date] = None
+    patient_age: str = ""
+    patient_sex: PatientSex = PatientSex.EMPTY
+    study_date: Optional[datetime.date] = None
+    study_instance_uid: str = ""
+    series_instance_uid: str = ""
+    study_description: str = ""
+    series_description: str = ""
 
 
 @dataclass(frozen=True)
@@ -266,7 +268,9 @@ def voxel_depth_mm(self) -> Optional[float]:
             return None
 
     def generate_extra_metadata(self,) -> Dict[str, Any]:
-        extra_metadata = {md.field_name: None for md in EXTRA_METADATA}
+        extra_metadata = {
+            md.field_name: md.default_value for md in EXTRA_METADATA
+        }
         for md in EXTRA_METADATA:
             try:
                 value = str(self.image.GetMetaData(md.keyword))
@@ -365,7 +369,7 @@ def save(self, output_directory: Path) -> Tuple[PanImg, Set[PanImgFile]]:
             window_center=None,
             window_width=None,
             eye_choice=self.eye_choice,
-            **{md.field_name: None for md in EXTRA_METADATA},
+            **{md.field_name: md.default_value for md in EXTRA_METADATA},
         )
 
         shutil.copy(src=self.file, dst=output_file)

pyproject.toml

@@ -31,7 +31,7 @@ commands =
 
 [tool.poetry]
 name = "panimg"
-version = "0.5.0"
+version = "0.5.1"
 description = "Conversion of medical images to MHA and TIFF."
 license = "Apache-2.0"
 authors = ["James Meakin <[email protected]>"]

tests/test_models.py

@@ -4,7 +4,7 @@
 
 from panimg.exceptions import ValidationError
 from panimg.image_builders.metaio_utils import load_sitk_image
-from panimg.models import ExtraMetaData, SimpleITKImage
+from panimg.models import EXTRA_METADATA, ExtraMetaData, SimpleITKImage
 from tests import RESOURCE_PATH
 
 
@@ -51,7 +51,7 @@
     ),
 )
 def test_dicom_vr_validation(vr, valid, invalid):
-    md = ExtraMetaData("Test", vr, "test")
+    md = ExtraMetaData("Test", vr, "test", "default")
     for t in valid:
         md.validate_value(t)
 
@@ -90,3 +90,21 @@ def test_built_image_invalid_headers(tmpdir, caplog, key, value):
     warning = caplog.records[0]
     assert warning.levelno == logging.WARNING
     assert "ValidationError" in warning.msg
+
+
+def test_built_image_extra_metadata_defaults(tmpdir, caplog):
+    src = RESOURCE_PATH / "image3x4.mhd"
+    sitk_image = load_sitk_image(src)
+    result = SimpleITKImage(
+        image=sitk_image,
+        name=src.name,
+        consumed_files={src},
+        spacing_valid=True,
+    )
+    new_image, new_files = result.save(output_directory=tmpdir)
+    assert len(caplog.records) == 0
+    expected_default_values = {
+        md.field_name: md.default_value for md in EXTRA_METADATA
+    }
+    for key, val in expected_default_values.items():
+        assert getattr(new_image, key) == val

tests/test_panimg.py

@@ -2,4 +2,4 @@
 
 
 def test_version():
-    assert __version__ == "0.5.0"
+    assert __version__ == "0.5.1"

tests/test_utils.py

@@ -62,7 +62,7 @@ def assert_img_properties(
             if md.keyword in md_keys:
                 assert value == md.cast_func(img.GetMetaData(md.keyword))
             else:
-                assert value is None
+                assert value is md.default_value
 
     img_ref = load_sitk_image(image)
     internal_image = SimpleITKImage(