Merge pull request #9 from qurit/8-optinal-fields

feat: make certain ds fields optional and test

rt_utils/ds_helper.py

@@ -68,22 +68,22 @@ def add_study_and_series_information(ds: FileDataset, series_data):
     ds.SeriesDate = reference_ds.SeriesDate
     ds.StudyTime = reference_ds.StudyTime
     ds.SeriesTime = reference_ds.SeriesTime
-    ds.StudyDescription = reference_ds.StudyDescription
-    ds.SeriesDescription = reference_ds.SeriesDescription
+    ds.StudyDescription = getattr(reference_ds, 'StudyDescription', '')
+    ds.SeriesDescription = getattr(reference_ds, 'SeriesDescription', '')
     ds.StudyInstanceUID = reference_ds.StudyInstanceUID
     ds.SeriesInstanceUID = generate_uid() # TODO: find out if random generation is ok
     ds.StudyID = reference_ds.StudyID
     ds.SeriesNumber = "1" # TODO: find out if we can just use 1 (Should be fine since its a new series)
 
 def add_patient_information(ds: FileDataset, series_data):
     reference_ds = series_data[0] # All elements in series should have the same data
-    ds.PatientName = reference_ds.PatientName
-    ds.PatientID = reference_ds.PatientID
-    ds.PatientBirthDate = reference_ds.PatientBirthDate
-    ds.PatientSex = reference_ds.PatientSex
-    ds.PatientAge = reference_ds.PatientAge
-    ds.PatientSize = reference_ds.PatientSize
-    ds.PatientWeight = reference_ds.PatientWeight
+    ds.PatientName = getattr(reference_ds, 'PatientName', '')
+    ds.PatientID = getattr(reference_ds, 'PatientID', '')
+    ds.PatientBirthDate = getattr(reference_ds, 'PatientBirthDate', '')
+    ds.PatientSex = getattr(reference_ds, 'PatientSex', '')
+    ds.PatientAge = getattr(reference_ds, 'PatientAge', '')
+    ds.PatientSize = getattr(reference_ds, 'PatientSize', '')
+    ds.PatientWeight = getattr(reference_ds, 'PatientWeight', '')
 
 
 def add_refd_frame_of_ref_sequence(ds: FileDataset, series_data):

setup.py

@@ -1,6 +1,6 @@
 import setuptools
 
-VERSION = '1.0.3'
+VERSION = '1.0.4'
 with open("README.md", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 with open('requirements.txt') as f:

tests/conftest.py

@@ -0,0 +1,20 @@
+from rt_utils.rtstruct import RTStruct
+import pytest
+import os
+from rt_utils import RTStructBuilder
+
+@pytest.fixture()
+def series_path() -> str:
+    return get_and_test_series_path()
+
+@pytest.fixture()
+def new_rtstruct() -> RTStruct:
+    path = get_and_test_series_path()
+    rtstruct = RTStructBuilder.create_new(path)
+    return rtstruct
+
+def get_and_test_series_path() -> str:
+    series_path = os.path.join(os.path.dirname(__file__), 'mock_data/')
+    assert os.path.exists(series_path)
+    return series_path
+

tests/test_ds_helper.py

@@ -0,0 +1,27 @@
+import pytest
+from rt_utils import ds_helper, image_helper
+
+def test_correctly_acquire_optional_ds_field(series_path):
+    series_data = image_helper.load_sorted_image_series(series_path)
+
+    patient_age = series_data[0]['PatientAge'].value    
+    ds = ds_helper.create_rtstruct_dataset(series_data)
+
+    assert ds.PatientAge == patient_age
+
+def test_ds_creation_without_patient_age(series_path):
+    # Ensure only 1 file in series data so ds_helper uses the file for header reference
+    series_data = image_helper.load_sorted_image_series(series_path)
+    series_data = [series_data[0]]
+
+    # Remove optional field
+    original_age = series_data[0]['PatientAge'].value
+    del series_data[0]['PatientAge']
+    with pytest.raises(Exception):
+        access = series_data[0]['PatientAge']
+
+    ds = ds_helper.create_rtstruct_dataset(series_data)
+
+    assert ds.PatientAge != original_age
+    assert ds.PatientAge == ''
+

tests/test_rtstruct_builder.py

@@ -75,17 +75,17 @@ def test_get_invalid_roi_mask_by_name(new_rtstruct: RTStruct):
         new_rtstruct.get_roi_mask_by_name("FAKE_NAME")
 
 
-def test_loading_invalid_rt_struct():
-    invalid_rt_struct_path = os.path.join(get_series_path(), 'ct_1.dcm')
+def test_loading_invalid_rt_struct(series_path):
+    invalid_rt_struct_path = os.path.join(series_path, 'ct_1.dcm')
     assert os.path.exists(invalid_rt_struct_path)
     with pytest.raises(Exception):
-        RTStructBuilder.create_from(get_series_path(), invalid_rt_struct_path)
+        RTStructBuilder.create_from(series_path, invalid_rt_struct_path)
 
 
-def test_loading_valid_rt_struct():
-    valid_rt_struct_path = os.path.join(get_series_path(), 'rt.dcm')
+def test_loading_valid_rt_struct(series_path):
+    valid_rt_struct_path = os.path.join(series_path, 'rt.dcm')
     assert os.path.exists(valid_rt_struct_path)
-    rtstruct = RTStructBuilder.create_from(get_series_path(), valid_rt_struct_path)
+    rtstruct = RTStructBuilder.create_from(series_path, valid_rt_struct_path)
 
     # Tests existing values predefined in the file are found
     assert hasattr(rtstruct.ds, 'ROIContourSequence')
@@ -157,13 +157,3 @@ def get_empty_mask(rtstruct) -> np.ndarray:
     mask = np.zeros(mask_dims)
     return mask.astype(bool)
 
-def get_series_path():
-    series_path = os.path.join(os.path.dirname(__file__), 'mock_data')
-    assert os.path.exists(series_path)
-    return series_path
-
-
-@pytest.fixture
-def new_rtstruct() -> RTStruct:
-    rtstruct = RTStructBuilder.create_new(get_series_path())
-    return rtstruct