Enhancement for API use

rt_utils/rtstruct.py

@@ -1,9 +1,12 @@
+from io import BytesIO
 from typing import List, Union
 
 import numpy as np
+import pydicom
 from pydicom.dataset import FileDataset
 
 from rt_utils.utils import ROIData
+
 from . import ds_helper, image_helper
 
 
@@ -133,6 +136,15 @@ def save(self, file_path: str):
             file.close()
         except OSError:
             raise Exception(f"Cannot write to file path '{file_path}'")
+
+    def save_to_memory(self):
+        """
+        Saves the RTStruct to a BytesIO stream and returns it.
+        """
+        buffer = BytesIO()
+        pydicom.dcmwrite(buffer, self.ds)
+        buffer.seek(0)  # Rewind the buffer for reading
+        return buffer
 
     class ROIException(Exception):
         """

rt_utils/rtstruct_builder.py

@@ -1,10 +1,11 @@
+import warnings
 from typing import List
+
 from pydicom.dataset import Dataset
 from pydicom.filereader import dcmread
 
-import warnings
-
 from rt_utils.utils import SOPClassUID
+
 from . import ds_helper, image_helper
 from .rtstruct import RTStruct
 
@@ -23,6 +24,17 @@ def create_new(dicom_series_path: str) -> RTStruct:
         series_data = image_helper.load_sorted_image_series(dicom_series_path)
         ds = ds_helper.create_rtstruct_dataset(series_data)
         return RTStruct(series_data, ds)
+
+    @staticmethod
+    def create_new_from_memory(dicom_datasets: List[Dataset]) -> RTStruct:
+        """
+         Method to generate a new rt struct from a DICOM series in memory already loaded by pydicom
+        """
+        # dicom_datasets are sorted by InstanceNumber
+        dicom_datasets.sort(key=lambda x: x.InstanceNumber if hasattr(x, 'InstanceNumber') else 0)
+
+        ds = ds_helper.create_rtstruct_dataset(dicom_datasets)
+        return RTStruct(dicom_datasets, ds)
 
     @staticmethod
     def create_from(dicom_series_path: str, rt_struct_path: str, warn_only: bool = False) -> RTStruct:
@@ -37,6 +49,17 @@ def create_from(dicom_series_path: str, rt_struct_path: str, warn_only: bool = F
 
         # TODO create new frame of reference? Right now we assume the last frame of reference created is suitable
         return RTStruct(series_data, ds)
+
+    @staticmethod
+    def create_from_memory(dicom_datasets: List[Dataset], existing_rt_struct: Dataset,  warn_only: bool = False) -> RTStruct :
+        """
+         Method to generate a new rt struct from a DICOM series and a RTStruct in memory already loaded by pydicom
+        """
+        dicom_datasets.sort(key=lambda x: x.InstanceNumber if hasattr(x, 'InstanceNumber') else 0)
+
+        RTStructBuilder.validate_rtstruct(existing_rt_struct)
+        RTStructBuilder.validate_rtstruct_series_references(existing_rt_struct, dicom_datasets, warn_only)
+        return RTStruct(dicom_datasets, existing_rt_struct)
 
     @staticmethod
     def validate_rtstruct(ds: Dataset):

tests/test_rtstruct_builder.py

@@ -6,7 +6,7 @@
 from rt_utils import image_helper
 from pydicom.dataset import validate_file_meta
 import numpy as np
-
+import pydicom
 
 def test_create_from_empty_series_dir():
     empty_dir_path = os.path.join(os.path.dirname(__file__), "empty")
@@ -251,3 +251,27 @@ def get_empty_mask(rtstruct) -> np.ndarray:
     )
     mask = np.zeros(mask_dims)
     return mask.astype(bool)
+
+def load_dicom_files_in_memory(file_paths):
+    dicom_datasets = []
+    for path in file_paths:
+        with open(path, 'rb') as f:
+            ds = pydicom.dcmread(f)
+            dicom_datasets.append(ds)
+    return dicom_datasets
+
+def test_create_rtstruct_from_memory():
+    print(os.getcwd())
+    dicom_files = load_dicom_files_in_memory(['tests/mock_data/ct_1.dcm', 'tests/mock_data/ct_2.dcm'])
+    rtstruct = RTStructBuilder.create_new_from_memory(dicom_files)
+    assert rtstruct is not None
+    assert len(rtstruct.series_data) == len(dicom_files)
+
+def test_save_rtstruct_to_memory():
+    dicom_files = load_dicom_files_in_memory(['tests/mock_data/ct_1.dcm', 'tests/mock_data/ct_2.dcm'])
+    rtstruct = RTStructBuilder.create_new_from_memory(dicom_files)
+    buffer = rtstruct.save_to_memory()
+    assert buffer is not None
+    buffer.seek(0)  # Reset the buffer to the beginning for reading
+    loaded_ds = pydicom.dcmread(buffer)
+    assert loaded_ds is not None